SMTL ID : 3cf1.1

Structure of P97/vcp in complex with ADP/ADP.alfx

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 4.40 Å

Oligo State

homo-hexamer

Ligands

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

ADP.1: 17 residues within 4Å: Chain A: D.205, I.206, G.207, P.247, G.248, T.249, G.250, K.251, T.252, L.253, D.304, I.380, H.384, G.408, A.409 Chain F: K.236, R.359 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain F Hydrogen bonds: A:G.207, A:G.207, A:G.248, A:G.250, A:K.251, A:T.252, A:T.252, A:L.253, F:K.236, F:R.359 Salt bridges: A:K.251, F:R.359 ADP.2: 13 residues within 4Å: Chain A: D.478, I.479, G.521, C.522, G.523, K.524, T.525, L.526, I.656, G.684, A.685, T.688 Ligands: AF3.3 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:I.479, A:G.521, A:C.522, A:G.523, A:K.524, A:T.525, A:T.525, A:L.526, A:T.688 ADP.4: 17 residues within 4Å: Chain A: K.236, R.359 Chain B: D.205, I.206, G.207, P.247, G.248, T.249, G.250, K.251, T.252, L.253, D.304, I.380, H.384, G.408, A.409 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.207, B:G.207, B:G.248, B:G.250, B:K.251, B:T.252, B:T.252, B:L.253, A:K.236 Salt bridges: B:K.251, A:R.359 ADP.5: 14 residues within 4Å: Chain B: D.478, I.479, G.521, C.522, G.523, K.524, T.525, L.526, I.656, N.660, G.684, A.685, T.688 Ligands: AF3.6 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:I.479, B:G.521, B:C.522, B:G.523, B:K.524, B:T.525, B:L.526, B:N.660, B:T.688 Salt bridges: B:K.524 ADP.7: 15 residues within 4Å: Chain B: R.359 Chain C: D.205, I.206, G.207, P.247, G.248, T.249, G.250, K.251, T.252, L.253, D.304, H.384, G.408, A.409 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:G.207, C:G.207, C:G.248, C:G.250, C:K.251, C:T.252, C:T.252, C:L.253 Salt bridges: C:K.251, B:R.359 ADP.8: 14 residues within 4Å: Chain C: D.478, I.479, G.521, C.522, G.523, K.524, T.525, L.526, I.656, N.660, G.684, A.685, T.688 Ligands: AF3.9 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:G.521, C:C.522, C:G.523, C:K.524, C:T.525, C:L.526, C:T.688 ADP.10: 17 residues within 4Å: Chain C: K.236, R.359 Chain D: D.205, I.206, G.207, P.247, G.248, T.249, G.250, K.251, T.252, L.253, D.304, I.380, H.384, G.408, A.409 12 PLIP interactions: 9 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:G.207, D:G.207, D:G.248, D:G.250, D:K.251, D:T.252, D:T.252, D:L.253, C:K.236, C:R.359 Salt bridges: D:K.251, C:R.359 ADP.11: 13 residues within 4Å: Chain D: D.478, I.479, G.521, C.522, G.523, K.524, T.525, L.526, I.656, G.684, A.685, T.688 Ligands: AF3.12 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:I.479, D:G.521, D:C.522, D:G.523, D:K.524, D:T.525, D:T.525, D:L.526, D:T.688 ADP.13: 17 residues within 4Å: Chain D: K.236, R.359 Chain E: D.205, I.206, G.207, P.247, G.248, T.249, G.250, K.251, T.252, L.253, D.304, I.380, H.384, G.408, A.409 11 PLIP interactions: 9 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:G.207, E:G.207, E:G.248, E:G.250, E:K.251, E:T.252, E:T.252, E:L.253, D:K.236 Salt bridges: E:K.251, D:R.359 ADP.14: 14 residues within 4Å: Chain E: D.478, I.479, G.521, C.522, G.523, K.524, T.525, L.526, I.656, N.660, G.684, A.685, T.688 Ligands: AF3.15 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:I.479, E:G.521, E:C.522, E:G.523, E:K.524, E:T.525, E:L.526, E:N.660, E:T.688 Salt bridges: E:K.524 ADP.16: 15 residues within 4Å: Chain E: R.359 Chain F: D.205, I.206, G.207, P.247, G.248, T.249, G.250, K.251, T.252, L.253, D.304, H.384, G.408, A.409 10 PLIP interactions: 9 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:G.207, F:G.207, F:G.248, F:G.250, F:K.251, F:T.252, F:T.252, F:L.253 Salt bridges: F:K.251, E:R.359 ADP.17: 14 residues within 4Å: Chain F: D.478, I.479, G.521, C.522, G.523, K.524, T.525, L.526, I.656, N.660, G.684, A.685, T.688 Ligands: AF3.18 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:G.521, F:C.522, F:G.523, F:K.524, F:T.525, F:L.526, F:T.688

6 x AF3: ALUMINUM FLUORIDE(Non-covalent)

AF3.3: 8 residues within 4Å: Chain A: P.519, P.520, G.521, C.522, K.524, T.525, A.622 Ligands: ADP.2 No protein-ligand interaction detected (PLIP) AF3.6: 9 residues within 4Å: Chain B: G.518, P.519, P.520, G.521, C.522, G.523, K.524, T.525 Ligands: ADP.5 No protein-ligand interaction detected (PLIP) AF3.9: 8 residues within 4Å: Chain C: P.519, P.520, G.521, C.522, G.523, K.524, T.525 Ligands: ADP.8 No protein-ligand interaction detected (PLIP) AF3.12: 8 residues within 4Å: Chain D: P.519, P.520, G.521, C.522, K.524, T.525, A.622 Ligands: ADP.11 No protein-ligand interaction detected (PLIP) AF3.15: 9 residues within 4Å: Chain E: G.518, P.519, P.520, G.521, C.522, G.523, K.524, T.525 Ligands: ADP.14 No protein-ligand interaction detected (PLIP) AF3.18: 8 residues within 4Å: Chain F: P.519, P.520, G.521, C.522, G.523, K.524, T.525 Ligands: ADP.17 No protein-ligand interaction detected (PLIP)

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
A

B
B

C
C

D
A

E
B

F
C

Transitional endoplasmic reticulum ATPase

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