SMTL ID : 7vcu.1

Human p97 double hexamer conformer I with D1-ATPgammaS and D2-ADP bound

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-12-mer

Ligands

12 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.1: 15 residues within 4Å: Chain A: D.205, I.206, G.207, G.248, T.249, G.250, K.251, T.252, L.253, N.348, I.380, G.408, A.409 Chain L: R.359 Ligands: MG.2 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:G.207, A:G.207, A:G.248, A:T.249, A:G.250, A:K.251, A:K.251, A:T.252, A:T.252, A:T.252, A:L.253, A:N.348, A:G.408 Salt bridges: A:K.251 AGS.4: 14 residues within 4Å: Chain B: D.205, I.206, G.207, G.248, T.249, G.250, K.251, T.252, L.253, N.348, I.380, G.408, A.409 Ligands: MG.5 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:G.207, B:G.207, B:G.248, B:T.249, B:G.250, B:K.251, B:K.251, B:T.252, B:T.252, B:T.252, B:L.253, B:N.348, B:G.408 Salt bridges: B:K.251 AGS.7: 14 residues within 4Å: Chain C: D.205, I.206, G.207, G.248, T.249, G.250, K.251, T.252, L.253, N.348, I.380, G.408, A.409 Ligands: MG.8 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:G.207, C:G.207, C:G.248, C:T.249, C:G.250, C:K.251, C:K.251, C:T.252, C:T.252, C:T.252, C:L.253, C:N.348, C:G.408 Salt bridges: C:K.251 AGS.10: 14 residues within 4Å: Chain D: D.205, I.206, G.207, G.248, T.249, G.250, K.251, T.252, L.253, N.348, I.380, G.408, A.409 Ligands: MG.11 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:G.207, D:G.207, D:G.248, D:T.249, D:G.250, D:K.251, D:K.251, D:T.252, D:T.252, D:T.252, D:L.253, D:N.348, D:G.408 Salt bridges: D:K.251 AGS.13: 15 residues within 4Å: Chain D: R.359 Chain E: D.205, I.206, G.207, G.248, T.249, G.250, K.251, T.252, L.253, N.348, I.380, G.408, A.409 Ligands: MG.14 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:G.207, E:G.207, E:G.248, E:T.249, E:G.250, E:K.251, E:K.251, E:T.252, E:T.252, E:T.252, E:L.253, E:N.348, E:G.408 Salt bridges: E:K.251 AGS.16: 15 residues within 4Å: Chain E: R.359 Chain F: D.205, I.206, G.207, G.248, T.249, G.250, K.251, T.252, L.253, N.348, I.380, G.408, A.409 Ligands: MG.17 16 PLIP interactions: 2 interactions with chain E, 14 interactions with chain F Hydrogen bonds: E:K.236, E:K.236, F:G.207, F:G.207, F:G.248, F:T.249, F:G.250, F:K.251, F:K.251, F:T.252, F:T.252, F:T.252, F:L.253, F:N.348, F:G.408 Salt bridges: F:K.251 AGS.19: 14 residues within 4Å: Chain G: D.205, I.206, G.207, G.248, T.249, G.250, K.251, T.252, L.253, N.348, I.380, G.408, A.409 Ligands: MG.20 14 PLIP interactions: 14 interactions with chain G Hydrogen bonds: G:G.207, G:G.207, G:G.248, G:T.249, G:G.250, G:K.251, G:K.251, G:T.252, G:T.252, G:T.252, G:L.253, G:N.348, G:G.408 Salt bridges: G:K.251 AGS.22: 14 residues within 4Å: Chain H: D.205, I.206, G.207, G.248, T.249, G.250, K.251, T.252, L.253, N.348, I.380, G.408, A.409 Ligands: MG.23 14 PLIP interactions: 14 interactions with chain H Hydrogen bonds: H:G.207, H:G.207, H:G.248, H:T.249, H:G.250, H:K.251, H:K.251, H:T.252, H:T.252, H:T.252, H:L.253, H:N.348, H:G.408 Salt bridges: H:K.251 AGS.25: 16 residues within 4Å: Chain H: K.236, R.359 Chain I: D.205, I.206, G.207, G.248, T.249, G.250, K.251, T.252, L.253, N.348, I.380, G.408, A.409 Ligands: MG.26 17 PLIP interactions: 14 interactions with chain I, 3 interactions with chain H Hydrogen bonds: I:G.207, I:G.207, I:G.248, I:T.249, I:G.250, I:K.251, I:K.251, I:T.252, I:T.252, I:T.252, I:L.253, I:N.348, I:G.408, H:K.236, H:K.236, H:R.359 Salt bridges: I:K.251 AGS.28: 14 residues within 4Å: Chain J: D.205, I.206, G.207, G.248, T.249, G.250, K.251, T.252, L.253, N.348, I.380, G.408, A.409 Ligands: MG.29 14 PLIP interactions: 14 interactions with chain J Hydrogen bonds: J:G.207, J:G.207, J:G.248, J:T.249, J:G.250, J:K.251, J:K.251, J:T.252, J:T.252, J:T.252, J:L.253, J:N.348, J:G.408 Salt bridges: J:K.251 AGS.31: 14 residues within 4Å: Chain K: D.205, I.206, G.207, G.248, T.249, G.250, K.251, T.252, L.253, N.348, I.380, G.408, A.409 Ligands: MG.32 14 PLIP interactions: 14 interactions with chain K Hydrogen bonds: K:G.207, K:G.207, K:G.248, K:T.249, K:G.250, K:K.251, K:K.251, K:T.252, K:T.252, K:T.252, K:L.253, K:N.348, K:G.408 Salt bridges: K:K.251 AGS.34: 14 residues within 4Å: Chain L: D.205, I.206, G.207, G.248, T.249, G.250, K.251, T.252, L.253, N.348, I.380, G.408, A.409 Ligands: MG.35 14 PLIP interactions: 14 interactions with chain L Hydrogen bonds: L:G.207, L:G.207, L:G.248, L:T.249, L:G.250, L:K.251, L:K.251, L:T.252, L:T.252, L:T.252, L:L.253, L:N.348, L:G.408 Salt bridges: L:K.251

12 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.252, D.304 Ligands: AGS.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:T.252, A:D.304, A:D.304 MG.5: 3 residues within 4Å: Chain B: T.252, D.304 Ligands: AGS.4 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.304, B:D.304 MG.8: 3 residues within 4Å: Chain C: T.252, D.304 Ligands: AGS.7 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.304, C:D.304 MG.11: 3 residues within 4Å: Chain D: T.252, D.304 Ligands: AGS.10 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:T.252, D:D.304, D:D.304 MG.14: 3 residues within 4Å: Chain E: T.252, D.304 Ligands: AGS.13 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.304, E:D.304 MG.17: 3 residues within 4Å: Chain F: T.252, D.304 Ligands: AGS.16 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.304, F:D.304 MG.20: 3 residues within 4Å: Chain G: T.252, D.304 Ligands: AGS.19 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.304, G:D.304 MG.23: 3 residues within 4Å: Chain H: T.252, D.304 Ligands: AGS.22 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:T.252, H:D.304, H:D.304 MG.26: 3 residues within 4Å: Chain I: T.252, D.304 Ligands: AGS.25 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:T.252, I:D.304, I:D.304 MG.29: 3 residues within 4Å: Chain J: T.252, D.304 Ligands: AGS.28 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:D.304, J:D.304 MG.32: 3 residues within 4Å: Chain K: T.252, D.304 Ligands: AGS.31 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:D.304, K:D.304 MG.35: 3 residues within 4Å: Chain L: T.252, D.304 Ligands: AGS.34 2 PLIP interactions: 2 interactions with chain L Metal complexes: L:D.304, L:D.304

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

ADP.3: 12 residues within 4Å: Chain A: D.478, I.479, G.480, G.521, C.522, G.523, K.524, T.525, L.526, I.656, N.660, T.688 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.480, A:G.521, A:C.522, A:G.523, A:K.524, A:T.525, A:L.526 Salt bridges: A:K.524 ADP.6: 12 residues within 4Å: Chain B: D.478, I.479, G.480, G.521, C.522, G.523, K.524, T.525, L.526, I.656, N.660, T.688 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:D.478, B:G.480, B:G.521, B:C.522, B:G.523, B:K.524, B:T.525, B:T.525, B:T.525 Salt bridges: B:K.524 ADP.9: 13 residues within 4Å: Chain C: D.478, I.479, G.480, G.521, C.522, G.523, K.524, T.525, L.526, I.656, N.660, G.684, T.688 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:G.480, C:G.480, C:G.521, C:C.522, C:G.523, C:K.524, C:T.525, C:T.525, C:T.525, C:N.660 Salt bridges: C:K.524 ADP.12: 13 residues within 4Å: Chain D: D.478, I.479, G.480, G.521, C.522, G.523, K.524, T.525, L.526, I.656, N.660, G.684, T.688 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:G.480, D:G.480, D:G.521, D:C.522, D:G.523, D:K.524, D:T.525, D:T.525, D:T.525, D:N.660 Salt bridges: D:K.524 ADP.15: 13 residues within 4Å: Chain E: D.478, I.479, G.480, G.521, C.522, G.523, K.524, T.525, L.526, I.656, N.660, G.684, T.688 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:G.480, E:G.480, E:G.521, E:C.522, E:G.523, E:K.524, E:T.525, E:T.525, E:T.525, E:N.660 Salt bridges: E:K.524 ADP.18: 12 residues within 4Å: Chain F: D.478, I.479, G.480, G.521, C.522, G.523, K.524, T.525, L.526, I.656, N.660, T.688 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:G.480, F:G.521, F:C.522, F:G.523, F:K.524, F:T.525, F:T.525, F:T.525, F:L.526, F:N.660 Salt bridges: F:K.524 ADP.21: 12 residues within 4Å: Chain G: D.478, I.479, G.480, G.521, C.522, G.523, K.524, T.525, L.526, I.656, N.660, T.688 10 PLIP interactions: 10 interactions with chain G Hydrogen bonds: G:D.478, G:G.480, G:G.521, G:C.522, G:G.523, G:K.524, G:T.525, G:T.525, G:T.525 Salt bridges: G:K.524 ADP.24: 13 residues within 4Å: Chain H: D.478, I.479, G.480, G.521, C.522, G.523, K.524, T.525, L.526, I.656, N.660, G.684, T.688 9 PLIP interactions: 9 interactions with chain H Hydrogen bonds: H:G.480, H:G.480, H:G.521, H:C.522, H:G.523, H:K.524, H:T.525, H:N.660 Salt bridges: H:K.524 ADP.27: 12 residues within 4Å: Chain I: D.478, I.479, G.480, G.521, C.522, G.523, K.524, T.525, L.526, I.656, N.660, T.688 10 PLIP interactions: 10 interactions with chain I Hydrogen bonds: I:G.480, I:G.521, I:C.522, I:G.523, I:K.524, I:T.525, I:T.525, I:T.525, I:L.526 Salt bridges: I:K.524 ADP.30: 12 residues within 4Å: Chain J: D.478, I.479, G.480, G.521, C.522, G.523, K.524, T.525, L.526, I.656, N.660, T.688 8 PLIP interactions: 8 interactions with chain J Hydrogen bonds: J:D.478, J:G.480, J:G.521, J:C.522, J:G.523, J:K.524, J:T.525 Salt bridges: J:K.524 ADP.33: 13 residues within 4Å: Chain K: D.478, I.479, G.480, P.520, G.521, C.522, G.523, K.524, T.525, L.526, I.656, N.660, T.688 11 PLIP interactions: 11 interactions with chain K Hydrogen bonds: K:G.480, K:G.521, K:C.522, K:G.523, K:K.524, K:T.525, K:T.525, K:T.525, K:L.526, K:N.660 Salt bridges: K:K.524 ADP.36: 12 residues within 4Å: Chain L: D.478, I.479, G.480, G.521, C.522, G.523, K.524, T.525, L.526, I.656, N.660, T.688 8 PLIP interactions: 8 interactions with chain L Hydrogen bonds: L:G.480, L:G.521, L:C.522, L:G.523, L:K.524, L:T.525, L:L.526 Salt bridges: L:K.524

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gao, H. et al., Cryo-EM structures of human p97 double hexamer capture potentiated ATPase-competent state. Cell Discov (2022)

Release Date

2022-03-02

Peptides

Transitional endoplasmic reticulum ATPase: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
K

B
B

C
C

D
D

E
E

F
F

G
A

H
L

I
G

J
H

K
I

L
J

Transitional endoplasmic reticulum ATPase

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