SMTL ID : 3cf2.2 (1 other biounit)

Structure of P97/vcp in complex with ADP/AMP-PNP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

homo-hexamer

Ligands

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

ADP.1: 15 residues within 4Å: Chain A: D.205, G.207, C.209, G.248, T.249, G.250, K.251, T.252, L.253, I.380, H.384, G.408, A.409 Chain B: K.236, R.359 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.207, A:G.207, A:G.248, A:T.249, A:G.250, A:K.251, A:T.252, A:T.252, A:T.252, A:L.253, B:K.236 Salt bridges: A:K.251, B:R.359 ADP.3: 15 residues within 4Å: Chain B: D.205, G.207, C.209, G.248, T.249, G.250, K.251, T.252, L.253, I.380, H.384, G.408, A.409 Chain E: K.236, R.359 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain E Hydrogen bonds: B:G.207, B:G.207, B:G.248, B:T.249, B:G.250, B:K.251, B:T.252, B:T.252, B:T.252, B:L.253, E:K.236 Salt bridges: B:K.251, E:R.359 ADP.5: 15 residues within 4Å: Chain C: D.205, G.207, C.209, G.248, T.249, G.250, K.251, T.252, L.253, I.380, H.384, G.408, A.409 Chain D: K.236, R.359 13 PLIP interactions: 11 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:G.207, C:G.207, C:G.248, C:T.249, C:G.250, C:K.251, C:T.252, C:T.252, C:T.252, C:L.253, D:K.236 Salt bridges: C:K.251, D:R.359 ADP.7: 15 residues within 4Å: Chain A: K.236, R.359 Chain D: D.205, G.207, C.209, G.248, T.249, G.250, K.251, T.252, L.253, I.380, H.384, G.408, A.409 13 PLIP interactions: 11 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:G.207, D:G.207, D:G.248, D:T.249, D:G.250, D:K.251, D:T.252, D:T.252, D:T.252, D:L.253, A:K.236 Salt bridges: D:K.251, A:R.359 ADP.9: 15 residues within 4Å: Chain E: D.205, G.207, C.209, G.248, T.249, G.250, K.251, T.252, L.253, I.380, H.384, G.408, A.409 Chain F: K.236, R.359 13 PLIP interactions: 11 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:G.207, E:G.207, E:G.248, E:T.249, E:G.250, E:K.251, E:T.252, E:T.252, E:T.252, E:L.253, F:K.236 Salt bridges: E:K.251, F:R.359 ADP.11: 15 residues within 4Å: Chain C: K.236, R.359 Chain F: D.205, G.207, C.209, G.248, T.249, G.250, K.251, T.252, L.253, I.380, H.384, G.408, A.409 13 PLIP interactions: 2 interactions with chain C, 11 interactions with chain F Hydrogen bonds: C:K.236, F:G.207, F:G.207, F:G.248, F:T.249, F:G.250, F:K.251, F:T.252, F:T.252, F:T.252, F:L.253 Salt bridges: C:R.359, F:K.251

6 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.2: 15 residues within 4Å: Chain A: D.478, I.479, P.519, P.520, G.521, C.522, G.523, K.524, T.525, L.526, D.577, N.624, I.656, T.688 Chain B: R.635 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.521, A:C.522, A:G.523, A:K.524, A:K.524, A:T.525, A:T.525, A:T.525, A:L.526, A:N.624, A:N.624 ANP.4: 15 residues within 4Å: Chain B: D.478, I.479, P.519, P.520, G.521, C.522, G.523, K.524, T.525, L.526, D.577, N.624, I.656, T.688 Chain E: R.635 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:G.521, B:C.522, B:G.523, B:K.524, B:K.524, B:T.525, B:T.525, B:T.525, B:L.526, B:N.624, B:N.624 ANP.6: 15 residues within 4Å: Chain C: D.478, I.479, P.519, P.520, G.521, C.522, G.523, K.524, T.525, L.526, D.577, N.624, I.656, T.688 Chain D: R.635 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:G.521, C:C.522, C:G.523, C:K.524, C:K.524, C:T.525, C:T.525, C:T.525, C:L.526, C:N.624, C:N.624 ANP.8: 15 residues within 4Å: Chain A: R.635 Chain D: D.478, I.479, P.519, P.520, G.521, C.522, G.523, K.524, T.525, L.526, D.577, N.624, I.656, T.688 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:G.521, D:C.522, D:G.523, D:K.524, D:K.524, D:T.525, D:T.525, D:T.525, D:L.526, D:N.624, D:N.624 ANP.10: 15 residues within 4Å: Chain E: D.478, I.479, P.519, P.520, G.521, C.522, G.523, K.524, T.525, L.526, D.577, N.624, I.656, T.688 Chain F: R.635 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:G.521, E:C.522, E:G.523, E:K.524, E:K.524, E:T.525, E:T.525, E:T.525, E:L.526, E:N.624, E:N.624 ANP.12: 15 residues within 4Å: Chain C: R.635 Chain F: D.478, I.479, P.519, P.520, G.521, C.522, G.523, K.524, T.525, L.526, D.577, N.624, I.656, T.688 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:G.521, F:C.522, F:G.523, F:K.524, F:K.524, F:T.525, F:T.525, F:T.525, F:L.526, F:N.624, F:N.624

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Davies, J.M. et al., Improved structures of full-length p97, an AAA ATPase: implications for mechanisms of nucleotide-dependent conformational change. Structure (2008)

Release Date

2008-04-22

Peptides

Transitional endoplasmic reticulum ATPase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
C

D
D

E
C

F
D

Transitional endoplasmic reticulum ATPase

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