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 code
  • UNP_START | Start of UniProt sequence for given PDBe entries
  • UNP_END | End of UniProt sequence for given PDBe entries
  • PDBe_ID | Protein Data Bank code
  • CHAIN_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 accession
  • CONFORMER_DESCR | Short description of conformation, based on depositor's assessment of the protein/conformation
  • LIT_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 suitable CONFORMER_ID is provided in this column. Blank cells have no other likely conformation assignmnt and are therefore the same as in CONFORMER_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.

  1. 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.

  1. 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.

  2. All remaining entries were then manually curated by investigating each PDBe entry's corresponding publication, where available.

  3. 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.

  4. For some UniProt accessions, intermediary conformations were reported by the authors and these were noted in the dataset under the CONFORMER_DESCR column.

  5. Entries deposited in monomeric form but solved as a multimeric complex were also removed.

  6. 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

Curation flow diagram

Dataset summary

Benchmark dataset summary graphs
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