SMTL ID : 7rlj.1

Cryo-EM structure of human p97 bound to CB-5083 and ATPgS.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-12-mer

Ligands

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

AGS.1: 16 residues within 4Å: Chain A: D.185, G.187, P.227, G.228, T.229, G.230, K.231, T.232, L.233, D.284, E.285, I.363, H.364, G.388, A.389 Ligands: MG.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.187, A:G.228, A:T.229, A:G.230, A:K.231, A:T.232, A:T.232 Salt bridges: A:K.231 AGS.4: 17 residues within 4Å: Chain A: F.340 Chain B: D.185, G.187, P.227, G.228, T.229, G.230, K.231, T.232, L.233, D.284, E.285, I.363, H.364, G.388, A.389 Ligands: MG.5 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.187, B:G.228, B:T.229, B:G.230, B:K.231, B:T.232, B:T.232, A:F.340 Salt bridges: B:K.231 AGS.7: 16 residues within 4Å: Chain C: D.185, G.187, P.227, G.228, T.229, G.230, K.231, T.232, L.233, D.284, E.285, I.363, H.364, G.388, A.389 Ligands: MG.8 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:G.187, C:G.228, C:T.229, C:G.230, C:K.231, C:T.232, C:T.232, B:F.340 Salt bridges: C:K.231 AGS.10: 17 residues within 4Å: Chain C: F.340 Chain D: D.185, G.187, P.227, G.228, T.229, G.230, K.231, T.232, L.233, D.284, E.285, I.363, H.364, G.388, A.389 Ligands: MG.11 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:G.187, D:G.228, D:T.229, D:G.230, D:K.231, D:T.232, D:T.232, C:F.340 Salt bridges: D:K.231 AGS.13: 17 residues within 4Å: Chain D: F.340 Chain E: D.185, G.187, P.227, G.228, T.229, G.230, K.231, T.232, L.233, D.284, E.285, I.363, H.364, G.388, A.389 Ligands: MG.14 9 PLIP interactions: 8 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:G.187, E:G.228, E:T.229, E:G.230, E:K.231, E:T.232, E:T.232, D:F.340 Salt bridges: E:K.231 AGS.16: 16 residues within 4Å: Chain F: D.185, G.187, P.227, G.228, T.229, G.230, K.231, T.232, L.233, D.284, E.285, I.363, H.364, G.388, A.389 Ligands: MG.17 8 PLIP interactions: 8 interactions with chain F Hydrogen bonds: F:G.187, F:G.228, F:T.229, F:G.230, F:K.231, F:T.232, F:T.232 Salt bridges: F:K.231 AGS.19: 17 residues within 4Å: Chain G: D.185, G.187, P.227, G.228, T.229, G.230, K.231, T.232, L.233, D.284, E.285, I.363, H.364, G.388, A.389 Chain L: R.339 Ligands: MG.20 8 PLIP interactions: 8 interactions with chain G Hydrogen bonds: G:G.187, G:G.228, G:T.229, G:G.230, G:K.231, G:T.232, G:T.232 Salt bridges: G:K.231 AGS.22: 18 residues within 4Å: Chain G: R.339, F.340 Chain H: D.185, G.187, P.227, G.228, T.229, G.230, K.231, T.232, L.233, D.284, E.285, I.363, H.364, G.388, A.389 Ligands: MG.23 9 PLIP interactions: 8 interactions with chain H, 1 interactions with chain G Hydrogen bonds: H:G.187, H:G.228, H:T.229, H:G.230, H:K.231, H:T.232, H:T.232, G:F.340 Salt bridges: H:K.231 AGS.25: 18 residues within 4Å: Chain H: R.339, F.340 Chain I: D.185, G.187, P.227, G.228, T.229, G.230, K.231, T.232, L.233, D.284, E.285, I.363, H.364, G.388, A.389 Ligands: MG.26 9 PLIP interactions: 8 interactions with chain I, 1 interactions with chain H Hydrogen bonds: I:G.187, I:G.228, I:T.229, I:G.230, I:K.231, I:T.232, I:T.232, H:F.340 Salt bridges: I:K.231 AGS.28: 16 residues within 4Å: Chain J: D.185, G.187, P.227, G.228, T.229, G.230, K.231, T.232, L.233, D.284, E.285, I.363, H.364, G.388, A.389 Ligands: MG.29 9 PLIP interactions: 8 interactions with chain J, 1 interactions with chain I Hydrogen bonds: J:G.187, J:G.228, J:T.229, J:G.230, J:K.231, J:T.232, J:T.232, I:F.340 Salt bridges: J:K.231 AGS.31: 16 residues within 4Å: Chain K: D.185, G.187, P.227, G.228, T.229, G.230, K.231, T.232, L.233, D.284, E.285, I.363, H.364, G.388, A.389 Ligands: MG.32 9 PLIP interactions: 8 interactions with chain K, 1 interactions with chain J Hydrogen bonds: K:G.187, K:G.228, K:T.229, K:G.230, K:K.231, K:T.232, K:T.232, J:F.340 Salt bridges: K:K.231 AGS.34: 17 residues within 4Å: Chain K: F.340 Chain L: D.185, G.187, P.227, G.228, T.229, G.230, K.231, T.232, L.233, D.284, E.285, I.363, H.364, G.388, A.389 Ligands: MG.35 9 PLIP interactions: 8 interactions with chain L, 1 interactions with chain K Hydrogen bonds: L:G.187, L:G.228, L:T.229, L:G.230, L:K.231, L:T.232, L:T.232, K:F.340 Salt bridges: L:K.231

12 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: T.232, D.284 Ligands: AGS.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.232 MG.5: 3 residues within 4Å: Chain B: T.232, D.284 Ligands: AGS.4 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.232 MG.8: 3 residues within 4Å: Chain C: T.232, D.284 Ligands: AGS.7 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.232 MG.11: 3 residues within 4Å: Chain D: T.232, D.284 Ligands: AGS.10 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.232 MG.14: 3 residues within 4Å: Chain E: T.232, D.284 Ligands: AGS.13 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.232 MG.17: 3 residues within 4Å: Chain F: T.232, D.284 Ligands: AGS.16 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.232 MG.20: 3 residues within 4Å: Chain G: T.232, D.284 Ligands: AGS.19 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:T.232 MG.23: 3 residues within 4Å: Chain H: T.232, D.284 Ligands: AGS.22 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:T.232 MG.26: 3 residues within 4Å: Chain I: T.232, D.284 Ligands: AGS.25 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:T.232 MG.29: 3 residues within 4Å: Chain J: T.232, D.284 Ligands: AGS.28 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:T.232 MG.32: 3 residues within 4Å: Chain K: T.232, D.284 Ligands: AGS.31 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:T.232 MG.35: 3 residues within 4Å: Chain L: T.232, D.284 Ligands: AGS.34 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:T.232

12 x JDP: 1-[4-(benzylamino)-7,8-dihydro-5H-pyrano[4,3-d]pyrimidin-2-yl]-2-methyl-1H-indole-4-carboxamide(Non-covalent)

JDP.3: 11 residues within 4Å: Chain A: V.454, D.458, I.459, G.501, C.502, G.503, L.506, I.636, G.664, A.665, T.668 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.454, A:L.506, A:I.636 Hydrogen bonds: A:G.501 JDP.6: 10 residues within 4Å: Chain B: V.454, D.458, I.459, G.501, C.502, G.503, L.506, G.664, A.665, T.668 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.454, B:L.506 Hydrogen bonds: B:G.501 JDP.9: 10 residues within 4Å: Chain C: V.454, D.458, I.459, G.501, C.502, G.503, L.506, G.664, A.665, T.668 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.506 Hydrogen bonds: C:G.501 JDP.12: 11 residues within 4Å: Chain D: V.454, D.458, I.459, G.501, C.502, G.503, L.506, I.636, G.664, A.665, T.668 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:V.454, D:L.506, D:I.636 Hydrogen bonds: D:G.501, D:R.642 JDP.15: 11 residues within 4Å: Chain E: V.454, D.458, I.459, G.501, C.502, G.503, L.506, I.636, G.664, A.665, T.668 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:G.501 JDP.18: 10 residues within 4Å: Chain F: V.454, D.458, I.459, G.501, C.502, G.503, L.506, G.664, A.665, T.668 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:V.454, F:L.506 Hydrogen bonds: F:G.501 JDP.21: 11 residues within 4Å: Chain G: V.454, D.458, I.459, G.501, C.502, G.503, L.506, I.636, G.664, A.665, T.668 6 PLIP interactions: 6 interactions with chain G Hydrophobic interactions: G:V.454, G:L.506, G:I.636 Hydrogen bonds: G:G.501, G:R.642, G:T.668 JDP.24: 10 residues within 4Å: Chain H: V.454, D.458, I.459, G.501, C.502, G.503, L.506, G.664, A.665, T.668 5 PLIP interactions: 5 interactions with chain H Hydrophobic interactions: H:V.454, H:I.459, H:L.506 Hydrogen bonds: H:G.501, H:T.668 JDP.27: 10 residues within 4Å: Chain I: V.454, D.458, I.459, G.501, C.502, G.503, L.506, G.664, A.665, T.668 5 PLIP interactions: 5 interactions with chain I Hydrophobic interactions: I:V.454, I:I.459, I:L.506 Hydrogen bonds: I:G.501, I:T.668 JDP.30: 10 residues within 4Å: Chain J: V.454, D.458, I.459, G.501, C.502, G.503, L.506, G.664, A.665, T.668 5 PLIP interactions: 5 interactions with chain J Hydrophobic interactions: J:V.454, J:I.459, J:L.506 Hydrogen bonds: J:G.501, J:T.668 JDP.33: 11 residues within 4Å: Chain K: V.454, D.458, I.459, G.501, C.502, G.503, L.506, I.636, G.664, A.665, T.668 4 PLIP interactions: 4 interactions with chain K Hydrophobic interactions: K:V.454, K:L.506 Hydrogen bonds: K:G.501, K:T.668 JDP.36: 11 residues within 4Å: Chain L: V.454, D.458, I.459, G.501, C.502, G.503, L.506, I.636, G.664, A.665, T.668 4 PLIP interactions: 4 interactions with chain L Hydrophobic interactions: L:V.454, L:L.506 Hydrogen bonds: L:G.501, L:T.668

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Caffrey, B. et al., AAA+ ATPase p97/VCP mutants and inhibitor binding disrupt inter-domain coupling and subsequent allosteric activation. J.Biol.Chem. (2021)

Release Date

2021-09-22

Peptides

Transitional endoplasmic reticulum ATPase: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
L

H
G

I
H

J
I

K
J

L
K

Transitional endoplasmic reticulum ATPase

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