SMTL ID : 5kiy.1

p97 ND1-A232E in complex with VIMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.79 Å

Oligo State

hetero-6-6-mer

Ligands

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

ANP.1: 18 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, N.348, I.380, H.384, G.408, A.409 Chain I: R.359, F.360 Ligands: MG.2 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain I Hydrogen bonds: A:G.207, A:G.248, A:T.249, A:T.249, A:G.250, A:K.251, A:K.251, A:T.252, A:T.252, A:L.253, A:N.348, I:R.359 Water bridges: A:T.252, A:T.252, A:D.304, A:G.408 ANP.3: 18 residues within 4Å: Chain C: D.205, I.206, G.207, P.247, G.248, T.249, G.250, K.251, T.252, L.253, N.348, I.380, H.384, G.408, A.409 Chain K: R.359, F.360 Ligands: MG.4 16 PLIP interactions: 15 interactions with chain C, 1 interactions with chain K Hydrogen bonds: C:G.207, C:G.248, C:T.249, C:T.249, C:G.250, C:K.251, C:K.251, C:T.252, C:T.252, C:L.253, C:N.348, K:R.359 Water bridges: C:T.252, C:T.252, C:D.304, C:G.408 ANP.5: 18 residues within 4Å: Chain E: D.205, I.206, G.207, P.247, G.248, T.249, G.250, K.251, T.252, L.253, N.348, I.380, H.384, G.408, A.409 Chain G: R.359, F.360 Ligands: MG.6 16 PLIP interactions: 15 interactions with chain E, 1 interactions with chain G Hydrogen bonds: E:G.207, E:G.248, E:T.249, E:T.249, E:G.250, E:K.251, E:K.251, E:T.252, E:T.252, E:L.253, E:N.348, G:R.359 Water bridges: E:T.252, E:T.252, E:D.304, E:G.408 ANP.7: 18 residues within 4Å: Chain C: R.359, F.360 Chain G: D.205, I.206, G.207, P.247, G.248, T.249, G.250, K.251, T.252, L.253, N.348, I.380, H.384, G.408, A.409 Ligands: MG.8 16 PLIP interactions: 15 interactions with chain G, 1 interactions with chain C Hydrogen bonds: G:G.207, G:G.248, G:T.249, G:T.249, G:G.250, G:K.251, G:K.251, G:T.252, G:T.252, G:L.253, G:N.348, C:R.359 Water bridges: G:T.252, G:T.252, G:D.304, G:G.408 ANP.9: 18 residues within 4Å: Chain E: R.359, F.360 Chain I: D.205, I.206, G.207, P.247, G.248, T.249, G.250, K.251, T.252, L.253, N.348, I.380, H.384, G.408, A.409 Ligands: MG.10 16 PLIP interactions: 15 interactions with chain I, 1 interactions with chain E Hydrogen bonds: I:G.207, I:G.248, I:T.249, I:T.249, I:G.250, I:K.251, I:K.251, I:T.252, I:T.252, I:L.253, I:N.348, E:R.359 Water bridges: I:T.252, I:T.252, I:D.304, I:G.408 ANP.11: 18 residues within 4Å: Chain A: R.359, F.360 Chain K: D.205, I.206, G.207, P.247, G.248, T.249, G.250, K.251, T.252, L.253, N.348, I.380, H.384, G.408, A.409 Ligands: MG.12 16 PLIP interactions: 15 interactions with chain K, 1 interactions with chain A Hydrogen bonds: K:G.207, K:G.248, K:T.249, K:T.249, K:G.250, K:K.251, K:K.251, K:T.252, K:T.252, K:L.253, K:N.348, A:R.359 Water bridges: K:T.252, K:T.252, K:D.304, K:G.408

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.252, D.304 Ligands: ANP.1 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:T.252, H2O.1, H2O.1, H2O.1 MG.4: 3 residues within 4Å: Chain C: T.252, D.304 Ligands: ANP.3 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:T.252, H2O.1, H2O.1, H2O.2 MG.6: 3 residues within 4Å: Chain E: T.252, D.304 Ligands: ANP.5 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:T.252, H2O.2, H2O.2, H2O.3 MG.8: 3 residues within 4Å: Chain G: T.252, D.304 Ligands: ANP.7 4 PLIP interactions: 1 interactions with chain G, 3 Ligand-Water interactions Metal complexes: G:T.252, H2O.3, H2O.3, H2O.3 MG.10: 3 residues within 4Å: Chain I: T.252, D.304 Ligands: ANP.9 4 PLIP interactions: 1 interactions with chain I, 3 Ligand-Water interactions Metal complexes: I:T.252, H2O.4, H2O.4, H2O.4 MG.12: 3 residues within 4Å: Chain K: T.252, D.304 Ligands: ANP.11 4 PLIP interactions: 1 interactions with chain K, 3 Ligand-Water interactions Metal complexes: K:T.252, H2O.5, H2O.5, H2O.5

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tang, W.K. et al., Structural basis for nucleotide-modulated p97 association with the ER membrane. Cell Discov (2017)

Release Date

2017-12-20

Peptides

Transitional endoplasmic reticulum ATPase: ACEGIK
Selenoprotein S: BDFHJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

G
A

I
A

K
A

B
B

D
B

F
B

H
B

J
B

L
B

Transitional endoplasmic reticulum ATPase

Selenoprotein S

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