SMTL ID : 5ftm.1

Cryo-EM structure of human p97 bound to ATPgS (Conformation II)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.20 Å

Oligo State

homo-hexamer

Ligands

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

AGS.1: 17 residues within 4Å: Chain A: D.478, I.479, G.480, P.520, G.521, C.522, G.523, K.524, T.525, L.526, N.624, G.684, A.685, T.688 Chain F: R.635, R.766 Ligands: MG.3 13 PLIP interactions: 2 interactions with chain F, 11 interactions with chain A Hydrogen bonds: F:R.635, F:R.766, A:G.480, A:G.480, A:G.521, A:C.522, A:G.523, A:G.523, A:K.524, A:T.525, A:L.526, A:T.688 Salt bridges: A:K.524 AGS.4: 17 residues within 4Å: Chain A: R.635, R.766 Chain B: D.478, I.479, G.480, P.520, G.521, C.522, G.523, K.524, T.525, L.526, N.624, G.684, A.685, T.688 Ligands: MG.6 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.480, B:G.480, B:G.521, B:C.522, B:G.523, B:G.523, B:K.524, B:T.525, B:L.526, B:T.688, A:R.635, A:R.766 Salt bridges: B:K.524 AGS.7: 17 residues within 4Å: Chain B: R.635, R.766 Chain C: D.478, I.479, G.480, P.520, G.521, C.522, G.523, K.524, T.525, L.526, N.624, G.684, A.685, T.688 Ligands: MG.9 13 PLIP interactions: 11 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:G.480, C:G.480, C:G.521, C:C.522, C:G.523, C:G.523, C:K.524, C:T.525, C:L.526, C:T.688, B:R.635, B:R.766 Salt bridges: C:K.524 AGS.10: 17 residues within 4Å: Chain C: R.635, R.766 Chain D: D.478, I.479, G.480, P.520, G.521, C.522, G.523, K.524, T.525, L.526, N.624, G.684, A.685, T.688 Ligands: MG.12 13 PLIP interactions: 11 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:G.480, D:G.480, D:G.521, D:C.522, D:G.523, D:G.523, D:K.524, D:T.525, D:L.526, D:T.688, C:R.635, C:R.766 Salt bridges: D:K.524 AGS.13: 17 residues within 4Å: Chain D: R.635, R.766 Chain E: D.478, I.479, G.480, P.520, G.521, C.522, G.523, K.524, T.525, L.526, N.624, G.684, A.685, T.688 Ligands: MG.15 13 PLIP interactions: 11 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:G.480, E:G.480, E:G.521, E:C.522, E:G.523, E:G.523, E:K.524, E:T.525, E:L.526, E:T.688, D:R.635, D:R.766 Salt bridges: E:K.524 AGS.16: 17 residues within 4Å: Chain E: R.635, R.766 Chain F: D.478, I.479, G.480, P.520, G.521, C.522, G.523, K.524, T.525, L.526, N.624, G.684, A.685, T.688 Ligands: MG.18 13 PLIP interactions: 11 interactions with chain F, 2 interactions with chain E Hydrogen bonds: F:G.480, F:G.480, F:G.521, F:C.522, F:G.523, F:G.523, F:K.524, F:T.525, F:L.526, F:T.688, E:R.635, E:R.766 Salt bridges: F:K.524

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

ADP.2: 15 residues within 4Å: Chain A: D.205, I.206, 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: R.359 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:G.207, A:G.207, A:G.248, A:T.249, A:G.250, A:K.251, A:T.252, A:L.253 Salt bridges: A:K.251, F:R.359 ADP.5: 15 residues within 4Å: Chain A: R.359 Chain B: D.205, I.206, G.207, C.209, G.248, T.249, G.250, K.251, T.252, L.253, I.380, H.384, G.408, A.409 10 PLIP interactions: 1 interactions with chain A, 9 interactions with chain B Salt bridges: A:R.359, B:K.251 Hydrogen bonds: B:G.207, B:G.207, B:G.248, B:T.249, B:G.250, B:K.251, B:T.252, B:L.253 ADP.8: 15 residues within 4Å: Chain B: R.359 Chain C: D.205, I.206, G.207, C.209, G.248, T.249, G.250, K.251, T.252, L.253, I.380, 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:T.249, C:G.250, C:K.251, C:T.252, C:L.253 Salt bridges: C:K.251, B:R.359 ADP.11: 15 residues within 4Å: Chain C: R.359 Chain D: D.205, I.206, G.207, C.209, G.248, T.249, G.250, K.251, T.252, L.253, I.380, H.384, G.408, A.409 10 PLIP interactions: 1 interactions with chain C, 9 interactions with chain D Salt bridges: C:R.359, D:K.251 Hydrogen bonds: D:G.207, D:G.207, D:G.248, D:T.249, D:G.250, D:K.251, D:T.252, D:L.253 ADP.14: 15 residues within 4Å: Chain D: R.359 Chain E: D.205, I.206, G.207, C.209, G.248, T.249, G.250, K.251, T.252, L.253, I.380, H.384, G.408, A.409 10 PLIP interactions: 9 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:G.207, E:G.207, E:G.248, E:T.249, E:G.250, E:K.251, E:T.252, E:L.253 Salt bridges: E:K.251, D:R.359 ADP.17: 15 residues within 4Å: Chain E: R.359 Chain F: D.205, I.206, G.207, C.209, G.248, T.249, G.250, K.251, T.252, L.253, I.380, 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:T.249, F:G.250, F:K.251, F:T.252, F:L.253 Salt bridges: F:K.251, E:R.359

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: T.525 Ligands: AGS.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.525 MG.6: 2 residues within 4Å: Chain B: T.525 Ligands: AGS.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.525 MG.9: 2 residues within 4Å: Chain C: T.525 Ligands: AGS.7 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.525 MG.12: 2 residues within 4Å: Chain D: T.525 Ligands: AGS.10 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.525 MG.15: 2 residues within 4Å: Chain E: T.525 Ligands: AGS.13 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.525 MG.18: 2 residues within 4Å: Chain F: T.525 Ligands: AGS.16 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.525

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Banerjee, S. et al., 2.3 A Resolution Cryo-Em Structure of Human P97 and Mechanism of Allosteric Inhibition. Science (2016)

Release Date

2016-01-27

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

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