SMTL ID : 4kln.1

Structure of p97 N-D1 A232E mutant in complex with ATPgS

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.62 Å

Oligo State

homo-hexamer

Ligands

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

AGS.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 B: R.359, F.360 Ligands: MG.2 11 PLIP interactions: 11 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:L.253 Water bridges: A:T.252 Salt bridges: A:K.251 AGS.3: 18 residues within 4Å: Chain B: 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 C: R.359, F.360 Ligands: MG.4 13 PLIP interactions: 13 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, B:N.348 Water bridges: B:G.408 Salt bridges: B:K.251 AGS.5: 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 D: R.359, F.360 Ligands: MG.6 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:G.207, C:G.248, C:T.249, 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 AGS.7: 18 residues within 4Å: Chain D: 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 E: R.359, F.360 Ligands: MG.8 11 PLIP interactions: 11 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:L.253, D:N.348 Salt bridges: D:K.251 AGS.9: 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 F: R.359, F.360 Ligands: MG.10 15 PLIP interactions: 15 interactions with chain E Hydrogen bonds: E:G.207, E:G.248, E:T.249, E:T.249, E:T.249, E:G.250, E:K.251, E:T.252, E:T.252, E:L.253 Water bridges: E:T.252, E:T.252, E:T.252, E:G.408 Salt bridges: E:K.251 AGS.11: 18 residues within 4Å: Chain A: R.359, F.360 Chain F: 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 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:G.207, F:G.248, F:T.249, F:T.249, F:T.249, F:G.250, F:K.251, F:T.252, F:L.253 Water bridges: F:T.252, F:T.252, F:T.252, F:G.408 Salt bridges: F:K.251

6 x MG: MAGNESIUM ION(Non-covalent)

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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tang, W.K. et al., Altered Intersubunit Communication Is the Molecular Basis for Functional Defects of Pathogenic p97 Mutants. J.Biol.Chem. (2013)

Release Date

2013-11-13

Peptides

Transitional endoplasmic reticulum ATPase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Transitional endoplasmic reticulum ATPase