Datasets:
Unnamed: 0
int64 0
369
| UNP_ACC
stringlengths 6
10
| UNP_START
int64 1
609
| UNP_END
int64 161
2.93k
| PDBe_ID
stringlengths 4
4
| CHAIN_ID
stringclasses 12
values | label_asym_id
stringclasses 12
values | CONFORMER_ID
int64 1
5
| CONFORMER_DESCR
stringclasses 15
values | LIT_CONFIRMED
int64 0
1
| ALT_CONFORMER_ID
float64 1
4
⌀ | ALT_CONFORMER_DESCR
nullclasses 5
values | NOTES
stringclasses 26
values |
---|---|---|---|---|---|---|---|---|---|---|---|---|
0 | A0A075Q0W3 | 39 | 678 | 6mka | A | A | 1 | open | 1 | 1 | null | The structures between open and beta-lactam-bound adopt similar conformations and the primary differences are localised to the catalytic pocket (oxyanion hole). Unlike the closed conformation, therefore, which demonstrates a larger inward domain movement, CONFORMER_IDs 1 and 2 are globally similar in structure and could potentially be placed into the same conformation if merited by the use case. |
1 | A0A075Q0W3 | 39 | 678 | 6mkf | A | A | 2 | open_liganded | 1 | 2 | null | The structures between open and beta-lactam-bound adopt similar conformations and the primary differences are localised to the catalytic pocket (oxyanion hole). Unlike the closed conformation, therefore, which demonstrates a larger inward domain movement, CONFORMER_IDs 1 and 2 are globally similar in structure and could potentially be placed into the same conformation if merited by the use case. |
2 | A0A075Q0W3 | 39 | 678 | 6mkg | A | A | 2 | open_liganded | 1 | 2 | null | The structures between open and beta-lactam-bound adopt similar conformations and the primary differences are localised to the catalytic pocket (oxyanion hole). Unlike the closed conformation, therefore, which demonstrates a larger inward domain movement, CONFORMER_IDs 1 and 2 are globally similar in structure and could potentially be placed into the same conformation if merited by the use case. |
3 | A0A075Q0W3 | 39 | 678 | 6mkj | A | A | 3 | closed | 1 | 3 | null | Closed conformation exhibits a relatively large inter-domain movement, bringing the N1 and N2 domains closer together, in contrast to binding of the other beta-lactams in 6mkg and 6mkf |
4 | A0A1J6PWI8 | 20 | 273 | 6jmx | A | A | 1 | open | 1 | 1 | null | null |
5 | A0A1J6PWI8 | 20 | 273 | 6jn8 | A | A | 1 | open | 1 | 1 | null | null |
6 | A0A1J6PWI8 | 20 | 273 | 6jmy | A | A | 2 | closed | 1 | 2 | null | null |
7 | A0A1J6PWI8 | 20 | 273 | 6jn7 | A | A | 2 | closed | 1 | 2 | null | null |
8 | A0A1J6PWI8 | 20 | 273 | 6jn7 | B | B | 2 | closed | 1 | 2 | null | null |
9 | A0A1J6PWI8 | 20 | 273 | 6jn7 | C | C | 2 | closed | 1 | 2 | null | null |
10 | A0A1J6PWI8 | 20 | 273 | 6kv1 | A | A | 2 | closed | 1 | 2 | null | null |
11 | A0QTT2 | 1 | 439 | 7cy2 | A | A | 1 | open | 1 | 1 | null | null |
12 | A0QTT2 | 1 | 439 | 7cyr | A | A | 2 | closed | 1 | 2 | null | null |
13 | A0R629 | 13 | 412 | 5eqd | B | B | 1 | open | 0 | 1 | null | Pairwise RMSD comparison between chains in 5eqd and 5er9 show the two conformations in the asymmetric unit are different but identification of the closed and open structures is not possible alone. The open conformation is also nearly identical to the mixed conformation, with an RMSD of 0.000012 A over392 residues. |
14 | A0R629 | 13 | 412 | 5eqd | A | A | 2 | closed | 0 | 2 | null | Pairwise RMSD comparison between chains in 5eqd and 5er9 show the two conformations in the asymmetric unit are different but identification of the closed and open structures is not possible alone. The open conformation is also nearly identical to the mixed conformation, with an RMSD of 0.000012 A over392 residues. |
15 | A0R629 | 13 | 412 | 5er9 | A | A | 2 | closed | 0 | 2 | null | Pairwise RMSD comparison between chains in 5eqd and 5er9 show the two conformations in the asymmetric unit are different but identification of the closed and open structures is not possible alone. The open conformation is also nearly identical to the mixed conformation, with an RMSD of 0.000012 A over392 residues. |
16 | A0R629 | 13 | 412 | 5er9 | B | B | 3 | mixed | 0 | 1 | null | Almost identical in structure to open conformation (CONFORMER_ID=2) |
17 | A2RJ53 | 24 | 600 | 3fto | A | A | 1 | open | 1 | null | null | null |
18 | A2RJ53 | 24 | 600 | 3drf | A | A | 2 | closed | 1 | null | null | Substrate = octapeptide |
19 | A2RJ53 | 24 | 600 | 3drg | A | A | 2 | closed | 1 | null | null | Substrate = nonapeptide |
20 | A6UVT1 | 1 | 342 | 6hac | A | A | 1 | open | 1 | null | null | null |
21 | A6UVT1 | 1 | 342 | 6hae | A | A | 2 | closed | 1 | null | null | null |
22 | A6UVT1 | 1 | 342 | 6hae | K | B | 2 | closed | 1 | null | null | null |
23 | A6UVT1 | 1 | 342 | 6hav | A | A | 2 | closed | 1 | null | null | null |
24 | B3EYN2 | 1 | 848 | 5ho2 | A | A | 1 | open | 0 | null | null | null |
25 | B3EYN2 | 1 | 848 | 5ho0 | A | A | 2 | closed | 0 | null | null | null |
26 | B7IE18 | 1 | 475 | 6nc7 | A | A | 1 | open_inward | 1 | null | null | null |
27 | B7IE18 | 1 | 475 | 6nc7 | B | B | 1 | open_inward | 1 | null | null | null |
28 | B7IE18 | 1 | 475 | 6nc8 | A | A | 2 | occluded_inward | 1 | null | null | null |
29 | B7IE18 | 1 | 475 | 6nc9 | A | A | 3 | occluded_outward | 1 | null | null | null |
30 | B7IE18 | 1 | 475 | 6nc6 | A | A | 4 | closed_outward | 1 | null | null | null |
31 | B7IE18 | 1 | 475 | 6nc6 | B | B | 4 | closed_outward | 1 | null | null | null |
32 | C7C425 | 1 | 418 | 6xcs | A | A | 1 | open | 1 | null | null | null |
33 | C7C425 | 1 | 418 | 6xcs | B | B | 1 | open | 1 | null | null | null |
34 | C7C425 | 1 | 418 | 6xcq | A | A | 2 | closed | 1 | null | null | null |
35 | G0S4S9 | 1 | 2,925 | 6sl1 | A | A | 1 | open | 1 | null | null | null |
36 | G0S4S9 | 1 | 2,925 | 6skz | A | A | 2 | closed | 1 | null | null | null |
37 | G0SB58 | 24 | 1,505 | 5mzo | A | A | 1 | open | 1 | null | null | null |
38 | G0SB58 | 24 | 1,505 | 5mu1 | A | A | 2 | intermediate | 1 | null | null | null |
39 | G0SB58 | 24 | 1,505 | 5n2j | A | A | 3 | closed | 1 | null | null | null |
40 | G0SB58 | 24 | 1,505 | 5n2j | B | B | 3 | closed | 1 | null | null | null |
41 | G0SB58 | 24 | 1,505 | 5nv4 | A | A | 3 | closed | 1 | null | null | Double Cys mutant to stabilise protein in the closed conformation |
42 | J9UN47 | 25 | 609 | 4psp | A | A | 1 | open | 1 | null | null | null |
43 | J9UN47 | 25 | 609 | 4psp | B | B | 1 | open | 1 | null | null | null |
44 | J9UN47 | 25 | 609 | 4psr | A | A | 1 | open | 1 | null | null | null |
45 | J9UN47 | 25 | 609 | 4psr | B | B | 1 | open | 1 | null | null | null |
46 | J9UN47 | 25 | 609 | 4ni3 | A | A | 2 | closed | 1 | null | null | null |
47 | J9UN47 | 25 | 609 | 4ni3 | B | B | 2 | closed | 1 | null | null | null |
48 | O34926 | 1 | 405 | 3nc3 | A | A | 1 | open | 1 | null | null | null |
49 | O34926 | 1 | 405 | 3nc5 | A | A | 1 | open | 1 | null | null | null |
50 | O34926 | 1 | 405 | 3nc5 | B | B | 1 | open | 1 | null | null | null |
51 | O34926 | 1 | 405 | 3nc3 | B | B | 2 | closed | 1 | null | null | null |
52 | O34926 | 1 | 405 | 3nc6 | A | A | 2 | closed | 1 | null | null | null |
53 | O34926 | 1 | 405 | 3nc6 | B | B | 2 | closed | 1 | null | null | null |
54 | O34926 | 1 | 405 | 3nc7 | A | A | 2 | closed | 1 | null | null | null |
55 | O34926 | 1 | 405 | 3nc7 | B | B | 2 | closed | 1 | null | null | null |
56 | O76728 | 1 | 715 | 4bp8 | A | A | 1 | open | 1 | null | null | Authors not sure if dimer is crystallisation artefact or biologically important. |
57 | O76728 | 1 | 715 | 4bp8 | B | B | 1 | open | 1 | null | null | Authors not sure if dimer is crystallisation artefact or biologically important. |
58 | O76728 | 1 | 715 | 4bp9 | A | A | 2 | closed | 1 | null | null | Substrate = tetrapeptide. Authors not sure if dimer is crystallisation artefact or biologically important. |
59 | O76728 | 1 | 715 | 4bp9 | B | B | 2 | closed | 1 | null | null | Substrate = tetrapeptide. Authors not sure if dimer is crystallisation artefact or biologically important. |
60 | O76728 | 1 | 715 | 4bp9 | C | C | 2 | closed | 1 | null | null | Substrate = tetrapeptide. Authors not sure if dimer is crystallisation artefact or biologically important. |
61 | O76728 | 1 | 715 | 4bp9 | D | D | 2 | closed | 1 | null | null | Substrate = tetrapeptide. Authors not sure if dimer is crystallisation artefact or biologically important. |
62 | O76728 | 1 | 715 | 4bp9 | E | E | 2 | closed | 1 | null | null | Substrate = tetrapeptide. Authors not sure if dimer is crystallisation artefact or biologically important. |
63 | O76728 | 1 | 715 | 4bp9 | F | F | 2 | closed | 1 | null | null | Substrate = tetrapeptide. Authors not sure if dimer is crystallisation artefact or biologically important. |
64 | P00558 | 1 | 417 | 2xe6 | A | A | 1 | open | 1 | null | null | null |
65 | P00558 | 1 | 417 | 2xe7 | A | A | 1 | open | 1 | null | null | null |
66 | P00558 | 1 | 417 | 2xe8 | A | A | 1 | open | 1 | null | null | null |
67 | P00558 | 1 | 417 | 2wzd | A | A | 2 | closed | 1 | null | null | null |
68 | P00558 | 1 | 417 | 2ybe | A | A | 2 | closed | 1 | null | null | null |
69 | P00558 | 1 | 417 | 4axx | A | A | 2 | closed | 1 | null | null | null |
70 | P00918 | 1 | 260 | 3m1q | A | A | 1 | open | 0 | null | null | null |
71 | P00918 | 1 | 260 | 3m1w | A | A | 2 | closed | 0 | null | null | null |
72 | P0A4G2 | 1 | 309 | 4uto | A | A | 1 | open | 1 | null | null | null |
73 | P0A4G2 | 1 | 309 | 4uto | B | B | 1 | open | 1 | null | null | null |
74 | P0A4G2 | 1 | 309 | 4utp | A | A | 2 | closed | 1 | null | null | null |
75 | P0A4G2 | 1 | 309 | 4utp | B | B | 2 | closed | 1 | null | null | null |
76 | P0CG48 | 609 | 684 | 3ns8 | A | A | 1 | open | 1 | null | null | null |
77 | P0CG48 | 609 | 684 | 3ns8 | B | B | 1 | open | 1 | null | null | null |
78 | P0CG48 | 609 | 684 | 2n2k | A | A | 2 | closed | 1 | null | null | null |
79 | P0CG48 | 609 | 684 | 2n2k | B | B | 2 | closed | 1 | null | null | null |
80 | P14902 | 15 | 403 | 7p0n | A | A | 1 | open | 1 | null | null | null |
81 | P14902 | 15 | 403 | 7p0n | B | B | 1 | open | 1 | null | null | Unclear whether the dashed out cells are true conformations in their defined states. The unformatted cells are definitely in their conformation as stated by the authors. |
82 | P14902 | 15 | 403 | 7p0n | C | C | 1 | open | 1 | null | null | null |
83 | P14902 | 15 | 403 | 7p0n | D | D | 1 | open | 1 | null | null | Unclear whether the dashed out cells are true conformations in their defined states. The unformatted cells are definitely in their conformation as stated by the authors. |
84 | P14902 | 15 | 403 | 7p0r | A | A | 2 | intermediate | 1 | null | null | Unclear whether the dashed out cells are true conformations in their defined states. The unformatted cells are definitely in their conformation as stated by the authors. |
85 | P14902 | 15 | 403 | 7p0r | B | B | 2 | intermediate | 1 | null | null | null |
86 | P14902 | 15 | 403 | 7p0r | C | C | 2 | intermediate | 1 | null | null | null |
87 | P14902 | 15 | 403 | 7p0r | D | D | 2 | intermediate | 1 | null | null | Unclear whether the dashed out cells are true conformations in their defined states. The unformatted cells are definitely in their conformation as stated by the authors. |
88 | P14902 | 15 | 403 | 7nge | A | A | 3 | closed | 1 | null | null | null |
89 | P14902 | 15 | 403 | 7nge | B | B | 3 | closed | 1 | null | null | null |
90 | P14902 | 15 | 403 | 7nge | C | C | 3 | closed | 1 | null | null | Unclear whether the dashed out cells are true conformations in their defined states. The unformatted cells are definitely in their conformation as stated by the authors. |
91 | P14902 | 15 | 403 | 7nge | D | D | 3 | closed | 1 | null | null | Unclear whether the dashed out cells are true conformations in their defined states. The unformatted cells are definitely in their conformation as stated by the authors. |
92 | P15291 | 126 | 398 | 2fy7 | A | A | 1 | open | 1 | null | null | null |
93 | P15291 | 126 | 398 | 2fya | A | A | 1 | open | 1 | null | null | null |
94 | P15291 | 126 | 398 | 2fyb | A | A | 1 | open | 1 | null | null | null |
95 | P15291 | 126 | 398 | 6fwu | A | A | 1 | open | 1 | null | null | Dimer |
96 | P15291 | 126 | 398 | 6fwu | B | B | 1 | open | 1 | null | null | Dimer |
97 | P15291 | 126 | 398 | 2fyc | B | B | 2 | closed | 1 | null | null | Complexed with lactalbumin |
98 | P15291 | 126 | 398 | 2fyc | D | D | 2 | closed | 1 | null | null | Complexed with lactalbumin |
99 | P15291 | 126 | 398 | 2fyd | B | B | 2 | closed | 1 | null | null | Complexed with lactalbumin |
Schema description:
The manually curated dataset of open-closed monomers is included here as benchmarking_monomeric_open_closed_conformers.csv
.
Column descriptions:
Schema description:
The manually curated dataset of open-closed monomers is included here as benchmarking_monomeric_open_closed_conformers.csv
.
Column descriptions:
UNP_ACC
| UniProt accession codeUNP_START
| Start of UniProt sequence for given PDBe entriesUNP_END
| End of UniProt sequence for given PDBe entriesPDBe_ID
| Protein Data Bank codeCHAIN_ID
| Author declared chain ID (char
)label_asym_id
| Programmatically assigned chain ID (char
)CONFORMER_ID
| Unique code for PDBe entries with distinct conformation, corresponding to a given UniProt accessionCONFORMER_DESCR
| Short description of conformation, based on depositor's assessment of the protein/conformationLIT_CONFIRMED
| True/false value based on whether a publication (scientific literature) was available for manually curating clusters. NB: Clusters with 0 in this field should be used with caution.ALT_CONFORMER_ID
| Where the publication for a structure is currently outstanding, an executive decision on the conformation classification is made. Where the literature is not explicit on the features of a given conformation, the second most suitableCONFORMER_ID
is provided in this column. Blank cells have no other likely conformation assignmnt and are therefore the same as inCONFORMER_ID
.ALT_CONFORMER_DESCR
| Description for conformation in alternative conformation ID.
Curation process
As of 09 Mar 2022, a manually curated dataset of monomeric protein conformations has been collated, containing 'open'-'closed' pairs as well as intermediary states defined by the authors of the entry.
- The PDBe was queried, through its Oracle DB, to find PDBe entries with 100 % sequence identity for a UniProt segment in both 'open' and 'closed' conformations, as stated in the entry's
TITLE
field. The query used:
select b.accession, b.unp_start, b.unp_end, a.id, a.title, d.id, d.title
from entry a, unp_entity b, unp_entity c, entry d, pdb_assembly e
where a.title like ‘%open%’ and d.title like ‘%close%’
and a.id = b.entry_id and d.id = c.entry_id and a.id != d.id
and b.accession = c.accession
and b.unp_start = c.unp_start
and b.unp_end = c.unp_end
and a.id = e.entry_id
and e.type = ‘homo’
and e.name = ‘monomer’
was written by Dr Sameer Velankar.
These results were cleaned to remove entries with 'open' or 'close' substrings in their
TITLE
fields that did not refer to conformation. The 'open' substring often appeared in ligand names in the entries'TITLE
field, such as in dichlorido(1,3-dimethylbenzimidaz ol-2-ylidene)(eta5-pentamethylcyclopentadienyl)rhodium(III) and 'close' in terms like discloses.All remaining entries were then manually curated by investigating each PDBe entry's corresponding publication, where available.
Additional PDBe entries submitted by the authors, which were missed in the original search due to a lack of 'open' or 'close' substrings in their
TITLE
field but stated as fitting one of the states in the publication, were added.For some UniProt accessions, intermediary conformations were reported by the authors and these were noted in the dataset under the
CONFORMER_DESCR
column.Entries deposited in monomeric form but solved as a multimeric complex were also removed.
PDBe entries, now clustered by author-stated conformation, were cross-referenced against the PDBe-KB's existing clustering algorithm (available on the Aggregate Views of Proteins page) to assess current conformer clustering success. These results are currently awaiting publication.
Curation process outline
Dataset summary
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