SMTL ID : 7wub.1

Cryo-EM structure of dodecamer P97

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-10-1-1-mer

Ligands

12 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 17 residues within 4Å: Chain A: D.185, G.187, G.188, P.227, G.228, T.229, G.230, K.231, T.232, L.233, D.284, I.360, I.363, H.364, G.388, A.389 Chain F: R.339 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:G.187, A:G.187, A:G.228, A:T.229, A:G.230, A:K.231, A:T.232, A:T.232, A:T.232, A:L.233, A:D.284, A:H.364 Salt bridges: A:K.231, F:R.339 ADP.3: 17 residues within 4Å: Chain A: R.339 Chain B: D.185, G.187, G.188, P.227, G.228, T.229, G.230, K.231, T.232, L.233, D.284, I.360, I.363, H.364, G.388, A.389 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.187, B:G.187, B:G.228, B:T.229, B:G.230, B:K.231, B:T.232, B:T.232, B:T.232, B:L.233, B:D.284, B:H.364 Salt bridges: B:K.231, A:R.339 ADP.5: 18 residues within 4Å: Chain B: R.339 Chain C: D.6, I.7, G.8, G.9, P.48, G.49, T.50, G.51, K.52, T.53, L.54, D.105, I.181, I.184, H.185, G.209, A.210 14 PLIP interactions: 13 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:G.8, C:G.8, C:G.49, C:T.50, C:G.51, C:K.52, C:T.53, C:T.53, C:T.53, C:L.54, C:D.105, C:H.185 Salt bridges: C:K.52, B:R.339 ADP.7: 17 residues within 4Å: Chain C: R.160 Chain D: D.6, G.8, G.9, P.48, G.49, T.50, G.51, K.52, T.53, L.54, D.105, I.181, I.184, H.185, G.209, A.210 13 PLIP interactions: 12 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:G.8, D:G.8, D:G.49, D:T.50, D:G.51, D:K.52, D:T.53, D:T.53, D:T.53, D:L.54, D:D.105 Salt bridges: D:K.52, C:R.160 ADP.9: 17 residues within 4Å: Chain D: R.160 Chain E: D.185, G.187, G.188, P.227, G.228, T.229, G.230, K.231, T.232, L.233, D.284, I.360, I.363, H.364, G.388, A.389 14 PLIP interactions: 13 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:G.187, E:G.187, E:G.228, E:T.229, E:G.230, E:K.231, E:T.232, E:T.232, E:T.232, E:L.233, E:D.284, E:H.364 Salt bridges: E:K.231, D:R.160 ADP.11: 18 residues within 4Å: Chain E: R.339 Chain F: D.185, I.186, G.187, G.188, P.227, G.228, T.229, G.230, K.231, T.232, L.233, D.284, I.360, I.363, H.364, G.388, A.389 13 PLIP interactions: 12 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:G.187, F:G.187, F:G.228, F:T.229, F:G.230, F:K.231, F:T.232, F:T.232, F:T.232, F:L.233, F:D.284 Salt bridges: F:K.231, E:R.339 ADP.13: 17 residues within 4Å: Chain G: D.185, G.187, G.188, C.189, G.228, T.229, G.230, K.231, T.232, L.233, I.360, I.363, H.364, G.388, A.389, A.392 Chain L: R.339 14 PLIP interactions: 13 interactions with chain G, 1 interactions with chain L Hydrogen bonds: G:G.187, G:G.228, G:T.229, G:T.229, G:T.229, G:T.229, G:G.230, G:K.231, G:T.232, G:T.232, G:L.233, G:A.389 Salt bridges: G:K.231, L:R.339 ADP.15: 17 residues within 4Å: Chain G: R.339 Chain H: D.185, G.187, G.188, C.189, G.228, T.229, G.230, K.231, T.232, L.233, I.360, I.363, H.364, G.388, A.389, A.392 14 PLIP interactions: 13 interactions with chain H, 1 interactions with chain G Hydrogen bonds: H:G.187, H:G.187, H:G.228, H:T.229, H:T.229, H:T.229, H:G.230, H:K.231, H:T.232, H:T.232, H:L.233, H:A.389 Salt bridges: H:K.231, G:R.339 ADP.17: 17 residues within 4Å: Chain H: R.339 Chain I: D.185, G.187, G.188, C.189, G.228, T.229, G.230, K.231, T.232, L.233, I.360, I.363, H.364, G.388, A.389, A.392 14 PLIP interactions: 13 interactions with chain I, 1 interactions with chain H Hydrogen bonds: I:G.187, I:G.187, I:G.228, I:T.229, I:T.229, I:T.229, I:G.230, I:K.231, I:T.232, I:T.232, I:L.233, I:A.389 Salt bridges: I:K.231, H:R.339 ADP.19: 16 residues within 4Å: Chain I: R.339 Chain J: D.185, G.187, G.188, G.228, T.229, G.230, K.231, T.232, L.233, I.360, I.363, H.364, G.388, A.389, A.392 14 PLIP interactions: 13 interactions with chain J, 1 interactions with chain I Hydrogen bonds: J:G.187, J:G.187, J:G.228, J:T.229, J:T.229, J:T.229, J:G.230, J:K.231, J:T.232, J:T.232, J:L.233, J:A.389 Salt bridges: J:K.231, I:R.339 ADP.21: 16 residues within 4Å: Chain J: R.339 Chain K: D.185, G.187, G.188, G.228, T.229, G.230, K.231, T.232, L.233, I.360, I.363, H.364, G.388, A.389, A.392 14 PLIP interactions: 13 interactions with chain K, 1 interactions with chain J Hydrogen bonds: K:G.187, K:G.228, K:T.229, K:T.229, K:T.229, K:T.229, K:G.230, K:K.231, K:T.232, K:T.232, K:L.233, K:A.389 Salt bridges: K:K.231, J:R.339 ADP.23: 17 residues within 4Å: Chain K: R.339 Chain L: D.185, G.187, G.188, C.189, G.228, T.229, G.230, K.231, T.232, L.233, I.360, I.363, H.364, G.388, A.389, A.392 14 PLIP interactions: 13 interactions with chain L, 1 interactions with chain K Hydrogen bonds: L:G.187, L:G.228, L:T.229, L:T.229, L:T.229, L:T.229, L:G.230, L:K.231, L:T.232, L:T.232, L:L.233, L:A.389 Salt bridges: L:K.231, K:R.339

12 x Y6Y: 3-[3-cyclopentylsulfanyl-5-[[3-methyl-4-(4-methylsulfonylphenyl)phenoxy]methyl]-1,2,4-triazol-4-yl]pyridine(Non-covalent)

Y6Y.2: 25 residues within 4Å: Chain A: L.472, V.473, P.476, V.477, P.480, F.483, L.484, G.487, M.488, T.489, P.490, S.491, K.492, C.515, A.517, P.551, C.552, V.553, K.595, N.596, F.598 Chain B: Q.378, E.382, R.433, K.643 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.473, A:P.476, A:V.477, A:L.484, A:P.490, A:K.492, A:A.517, A:K.595 Y6Y.4: 25 residues within 4Å: Chain B: L.472, V.473, P.476, V.477, P.480, F.483, L.484, G.487, M.488, T.489, P.490, S.491, K.492, C.515, A.517, P.551, C.552, V.553, K.595, N.596, F.598 Chain C: Q.199, E.203, R.254, K.464 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.473, B:P.476, B:V.477, B:L.484, B:P.490, B:K.492, B:A.517, B:K.595 Y6Y.6: 25 residues within 4Å: Chain C: L.293, V.294, P.297, V.298, P.301, F.304, L.305, G.308, M.309, T.310, P.311, S.312, K.313, C.336, A.338, P.372, C.373, V.374, K.416, N.417, F.419 Chain D: Q.199, E.203, R.254, K.464 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:V.294, C:P.297, C:V.298, C:L.305, C:P.311, C:K.313, C:A.338, C:K.416 Y6Y.8: 25 residues within 4Å: Chain D: L.293, V.294, P.297, V.298, P.301, F.304, L.305, G.308, M.309, T.310, P.311, S.312, K.313, C.336, A.338, P.372, C.373, V.374, K.416, N.417, F.419 Chain E: Q.378, E.382, R.433, K.643 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:V.294, D:P.297, D:V.298, D:L.305, D:P.311, D:K.313, D:A.338, D:K.416 Y6Y.10: 25 residues within 4Å: Chain E: L.472, V.473, P.476, V.477, P.480, F.483, L.484, G.487, M.488, T.489, P.490, S.491, K.492, C.515, A.517, P.551, C.552, V.553, K.595, N.596, F.598 Chain F: Q.378, E.382, R.433, K.643 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:V.473, E:P.476, E:V.477, E:L.484, E:P.490, E:K.492, E:A.517, E:K.595 Y6Y.12: 25 residues within 4Å: Chain A: Q.378, E.382, R.433, K.643 Chain F: L.472, V.473, P.476, V.477, P.480, F.483, L.484, G.487, M.488, T.489, P.490, S.491, K.492, C.515, A.517, P.551, C.552, V.553, K.595, N.596, F.598 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:V.473, F:P.476, F:V.477, F:L.484, F:P.490, F:K.492, F:A.517, F:K.595 Y6Y.14: 23 residues within 4Å: Chain G: L.472, V.473, P.476, V.477, P.480, F.483, L.484, G.487, M.488, T.489, P.490, S.491, K.492, C.515, A.517, P.551, C.552, V.553, K.595, N.596, F.598 Chain H: E.382, K.643 14 PLIP interactions: 14 interactions with chain G Hydrophobic interactions: G:V.473, G:V.477, G:F.483, G:L.484, G:L.484, G:P.490, G:K.492, G:K.492, G:A.517, G:P.551, G:V.553, G:K.595 Hydrogen bonds: G:N.596 pi-Cation interactions: G:K.595 Y6Y.16: 23 residues within 4Å: Chain H: L.472, V.473, P.476, V.477, P.480, F.483, L.484, G.487, M.488, T.489, P.490, S.491, K.492, C.515, A.517, P.551, C.552, V.553, K.595, N.596, F.598 Chain I: E.382, K.643 14 PLIP interactions: 14 interactions with chain H Hydrophobic interactions: H:V.473, H:V.477, H:F.483, H:L.484, H:L.484, H:P.490, H:K.492, H:K.492, H:A.517, H:P.551, H:V.553, H:K.595 Hydrogen bonds: H:N.596 pi-Cation interactions: H:K.595 Y6Y.18: 23 residues within 4Å: Chain I: L.472, V.473, P.476, V.477, P.480, F.483, L.484, G.487, M.488, T.489, P.490, S.491, K.492, C.515, A.517, P.551, C.552, V.553, K.595, N.596, F.598 Chain J: E.382, K.643 14 PLIP interactions: 14 interactions with chain I Hydrophobic interactions: I:V.473, I:V.477, I:F.483, I:L.484, I:L.484, I:P.490, I:K.492, I:K.492, I:A.517, I:P.551, I:V.553, I:K.595 Hydrogen bonds: I:N.596 pi-Cation interactions: I:K.595 Y6Y.20: 23 residues within 4Å: Chain J: L.472, V.473, P.476, V.477, P.480, F.483, L.484, G.487, M.488, T.489, P.490, S.491, K.492, C.515, A.517, P.551, C.552, V.553, K.595, N.596, F.598 Chain K: E.382, K.643 14 PLIP interactions: 14 interactions with chain J Hydrophobic interactions: J:V.473, J:V.477, J:F.483, J:L.484, J:L.484, J:P.490, J:K.492, J:K.492, J:A.517, J:P.551, J:V.553, J:K.595 Hydrogen bonds: J:N.596 pi-Cation interactions: J:K.595 Y6Y.22: 23 residues within 4Å: Chain K: L.472, V.473, P.476, V.477, P.480, F.483, L.484, G.487, M.488, T.489, P.490, S.491, K.492, C.515, A.517, P.551, C.552, V.553, K.595, N.596, F.598 Chain L: E.382, K.643 14 PLIP interactions: 14 interactions with chain K Hydrophobic interactions: K:V.473, K:V.477, K:F.483, K:L.484, K:L.484, K:P.490, K:K.492, K:K.492, K:A.517, K:P.551, K:V.553, K:K.595 Hydrogen bonds: K:N.596 pi-Cation interactions: K:K.595 Y6Y.24: 23 residues within 4Å: Chain G: E.382, K.643 Chain L: L.472, V.473, P.476, V.477, P.480, F.483, L.484, G.487, M.488, T.489, P.490, S.491, K.492, C.515, A.517, P.551, C.552, V.553, K.595, N.596, F.598 14 PLIP interactions: 14 interactions with chain L Hydrophobic interactions: L:V.473, L:V.477, L:F.483, L:L.484, L:L.484, L:P.490, L:K.492, L:K.492, L:A.517, L:P.551, L:V.553, L:K.595 Hydrogen bonds: L:N.596 pi-Cation interactions: L:K.595

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, S. et al., Cryo-EM structure of dodecamer P97 at 2.99 Angstroms resolution. To Be Published

Release Date

2022-03-23

Peptides

Transitional endoplasmic reticulum ATPase: ABEFGHIJKL
Transitional endoplasmic reticulum ATPase: C
Transitional endoplasmic reticulum ATPase: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

C
C

D
D

Transitional endoplasmic reticulum ATPase

Transitional endoplasmic reticulum ATPase

Transitional endoplasmic reticulum ATPase

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