SMTL ID : 8ooi.1

Full composite cryo-EM map of p97/VCP in ADP.Pi state

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

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

ADP.1: 16 residues within 4Å: Chain A: D.205, I.206, G.207, G.248, T.249, G.250, K.251, T.252, L.253, I.380, H.384, G.408, A.409 Ligands: MG.4, K.5, PO4.7 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:G.207, A:G.248, A:T.249, A:T.249, A:G.250, A:K.251, A:T.252, A:T.252, A:T.252, A:L.253 Water bridges: A:G.408 Salt bridges: A:K.251 ADP.8: 16 residues within 4Å: Chain B: D.205, I.206, G.207, G.248, T.249, G.250, K.251, T.252, L.253, I.380, H.384, G.408, A.409 Ligands: MG.11, K.12, PO4.31 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:G.207, B:G.248, B:T.249, B:T.249, B:G.250, B:K.251, B:T.252, B:T.252, B:T.252, B:L.253 Water bridges: B:G.408 Salt bridges: B:K.251 ADP.13: 16 residues within 4Å: Chain C: D.205, I.206, G.207, G.248, T.249, G.250, K.251, T.252, L.253, I.380, H.384, G.408, A.409 Ligands: PO4.6, MG.16, K.17 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:G.207, C:G.248, C:T.249, C:T.249, C:G.250, C:K.251, C:T.252, C:T.252, C:T.252, C:L.253 Water bridges: C:G.408 Salt bridges: C:K.251 ADP.19: 16 residues within 4Å: Chain D: D.205, I.206, G.207, G.248, T.249, G.250, K.251, T.252, L.253, I.380, H.384, G.408, A.409 Ligands: MG.22, K.23, PO4.25 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:G.207, D:G.248, D:T.249, D:T.249, D:G.250, D:K.251, D:T.252, D:T.252, D:T.252, D:L.253 Water bridges: D:G.408 Salt bridges: D:K.251 ADP.26: 16 residues within 4Å: Chain E: D.205, I.206, G.207, G.248, T.249, G.250, K.251, T.252, L.253, I.380, H.384, G.408, A.409 Ligands: PO4.18, MG.29, K.30 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:G.207, E:G.248, E:T.249, E:T.249, E:G.250, E:K.251, E:T.252, E:T.252, E:T.252, E:L.253 Water bridges: E:G.408 Salt bridges: E:K.251 ADP.32: 16 residues within 4Å: Chain F: D.205, I.206, G.207, G.248, T.249, G.250, K.251, T.252, L.253, I.380, H.384, G.408, A.409 Ligands: PO4.24, MG.35, K.36 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:G.207, F:G.248, F:T.249, F:T.249, F:G.250, F:K.251, F:T.252, F:T.252, F:T.252, F:L.253 Water bridges: F:G.408 Salt bridges: F:K.251

6 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.2: 20 residues within 4Å: Chain A: D.478, I.479, G.480, L.482, P.519, P.520, G.521, C.522, G.523, K.524, T.525, L.526, N.624, S.652, I.656, N.660, G.684, A.685, T.688 Ligands: MG.3 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:G.480, A:G.480, A:G.521, A:C.522, A:G.523, A:K.524, A:T.525, A:T.525, A:N.624, A:S.652, A:N.660 Salt bridges: A:K.524, A:K.524 ATP.9: 20 residues within 4Å: Chain B: D.478, I.479, G.480, L.482, P.519, P.520, G.521, C.522, G.523, K.524, T.525, L.526, N.624, S.652, I.656, N.660, G.684, A.685, T.688 Ligands: MG.10 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:G.480, B:G.480, B:G.521, B:C.522, B:G.523, B:K.524, B:T.525, B:T.525, B:N.624, B:S.652, B:N.660 Salt bridges: B:K.524, B:K.524 ATP.14: 20 residues within 4Å: Chain C: D.478, I.479, G.480, L.482, P.519, P.520, G.521, C.522, G.523, K.524, T.525, L.526, N.624, S.652, I.656, N.660, G.684, A.685, T.688 Ligands: MG.15 13 PLIP interactions: 13 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:N.624, C:S.652, C:N.660 Salt bridges: C:K.524, C:K.524 ATP.20: 20 residues within 4Å: Chain D: D.478, I.479, G.480, L.482, P.519, P.520, G.521, C.522, G.523, K.524, T.525, L.526, N.624, S.652, I.656, N.660, G.684, A.685, T.688 Ligands: MG.21 13 PLIP interactions: 13 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:N.624, D:S.652, D:N.660 Salt bridges: D:K.524, D:K.524 ATP.27: 20 residues within 4Å: Chain E: D.478, I.479, G.480, L.482, P.519, P.520, G.521, C.522, G.523, K.524, T.525, L.526, N.624, S.652, I.656, N.660, G.684, A.685, T.688 Ligands: MG.28 13 PLIP interactions: 13 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:N.624, E:S.652, E:N.660 Salt bridges: E:K.524, E:K.524 ATP.33: 20 residues within 4Å: Chain F: D.478, I.479, G.480, L.482, P.519, P.520, G.521, C.522, G.523, K.524, T.525, L.526, N.624, S.652, I.656, N.660, G.684, A.685, T.688 Ligands: MG.34 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:G.480, F:G.480, F:G.521, F:C.522, F:G.523, F:K.524, F:T.525, F:T.525, F:N.624, F:S.652, F:N.660 Salt bridges: F:K.524, F:K.524

12 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: K.524, T.525, D.577, A.622 Ligands: ATP.2 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.577, H2O.1 MG.4: 6 residues within 4Å: Chain A: K.251, T.252, D.304, A.346 Ligands: ADP.1, PO4.7 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.304 MG.10: 5 residues within 4Å: Chain B: K.524, T.525, D.577, A.622 Ligands: ATP.9 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.577, H2O.2 MG.11: 6 residues within 4Å: Chain B: K.251, T.252, D.304, A.346 Ligands: ADP.8, PO4.31 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.304 MG.15: 5 residues within 4Å: Chain C: K.524, T.525, D.577, A.622 Ligands: ATP.14 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.577, H2O.3 MG.16: 6 residues within 4Å: Chain C: K.251, T.252, D.304, A.346 Ligands: PO4.6, ADP.13 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.304 MG.21: 5 residues within 4Å: Chain D: K.524, T.525, D.577, A.622 Ligands: ATP.20 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.577, H2O.4 MG.22: 6 residues within 4Å: Chain D: K.251, T.252, D.304, A.346 Ligands: ADP.19, PO4.25 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.304 MG.28: 5 residues within 4Å: Chain E: K.524, T.525, D.577, A.622 Ligands: ATP.27 2 PLIP interactions: 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.577, H2O.5 MG.29: 6 residues within 4Å: Chain E: K.251, T.252, D.304, A.346 Ligands: PO4.18, ADP.26 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.304 MG.34: 5 residues within 4Å: Chain F: K.524, T.525, D.577, A.622 Ligands: ATP.33 2 PLIP interactions: 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.577, H2O.6 MG.35: 6 residues within 4Å: Chain F: K.251, T.252, D.304, A.346 Ligands: PO4.24, ADP.32 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.304

6 x K: POTASSIUM ION(Non-functional Binders)

K.5: 1 residues within 4Å: Ligands: ADP.1 No protein-ligand interaction detected (PLIP) K.12: 1 residues within 4Å: Ligands: ADP.8 No protein-ligand interaction detected (PLIP) K.17: 1 residues within 4Å: Ligands: ADP.13 No protein-ligand interaction detected (PLIP) K.23: 1 residues within 4Å: Ligands: ADP.19 No protein-ligand interaction detected (PLIP) K.30: 1 residues within 4Å: Ligands: ADP.26 No protein-ligand interaction detected (PLIP) K.36: 1 residues within 4Å: Ligands: ADP.32 No protein-ligand interaction detected (PLIP)

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.6: 8 residues within 4Å: Chain A: R.359 Chain C: P.247, G.248, K.251, D.304, N.348 Ligands: ADP.13, MG.16 7 PLIP interactions: 1 interactions with chain A, 6 interactions with chain C Salt bridges: A:R.359, C:K.251 Hydrogen bonds: C:G.248, C:D.304, C:N.348 Water bridges: C:K.251, C:E.305 PO4.7: 8 residues within 4Å: Chain A: P.247, G.248, K.251, D.304, N.348 Chain B: R.359 Ligands: ADP.1, MG.4 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.248, A:N.348 Water bridges: A:K.251, A:E.305 Salt bridges: A:K.251, B:R.359 PO4.18: 8 residues within 4Å: Chain C: R.359 Chain E: P.247, G.248, K.251, D.304, N.348 Ligands: ADP.26, MG.29 6 PLIP interactions: 5 interactions with chain E, 1 interactions with chain C Hydrogen bonds: E:G.248, E:N.348 Water bridges: E:K.251, E:E.305 Salt bridges: E:K.251, C:R.359 PO4.24: 8 residues within 4Å: Chain D: R.359 Chain F: P.247, G.248, K.251, D.304, N.348 Ligands: ADP.32, MG.35 7 PLIP interactions: 6 interactions with chain F, 1 interactions with chain D Hydrogen bonds: F:G.248, F:D.304, F:N.348 Water bridges: F:K.251, F:E.305 Salt bridges: F:K.251, D:R.359 PO4.25: 8 residues within 4Å: Chain D: P.247, G.248, K.251, D.304, N.348 Chain E: R.359 Ligands: ADP.19, MG.22 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:G.248, D:N.348 Water bridges: D:K.251, D:E.305 Salt bridges: D:K.251, E:R.359 PO4.31: 8 residues within 4Å: Chain B: P.247, G.248, K.251, D.304, N.348 Chain F: R.359 Ligands: ADP.8, MG.11 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain F Hydrogen bonds: B:G.248, B:D.304, B:N.348 Water bridges: B:K.251, B:E.305 Salt bridges: B:K.251, F:R.359

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shein, M. et al., Characterizing ATP processing by the AAA+ protein p97 at the atomic level. Nat.Chem. (2024)

Release Date

2024-01-31

Peptides

Transitional endoplasmic reticulum ATPase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
F

C
B

D
D

E
C

F
E

Transitional endoplasmic reticulum ATPase

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