SMTL ID : 7ln4.1

Cryo-EM structure of human p97 in complex with Npl4/Ufd1 and polyubiquitinated Ub-Eos (FOM, Class 3)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-1-mer

Ligands

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

ADP.1: 15 residues within 4Å: Chain A: D.478, I.479, G.480, P.519, P.520, G.521, C.522, G.523, K.524, T.525, L.526, I.656, G.684, A.685, T.688 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.480, A:G.480, A:P.519, A:G.521, A:C.522, A:G.523, A:K.524, A:T.525, A:T.688 Salt bridges: A:K.524 ADP.2: 15 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, I.380, H.384, A.409, A.412 Chain F: F.360 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.207, A:G.207, A:G.248, A:T.249, A:G.250, A:K.251 Salt bridges: A:K.251, A:K.251 ADP.4: 14 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, I.380, H.384, G.408, A.409 9 PLIP interactions: 9 interactions with chain B 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 Salt bridges: B:K.251 ADP.19: 16 residues within 4Å: Chain F: D.478, I.479, G.480, L.482, P.520, G.521, C.522, G.523, K.524, T.525, L.526, I.656, N.660, G.684, A.685, T.688 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:G.480, F:G.480, F:G.521, F:G.523, F:K.524, F:T.525, F:N.660, F:T.688 Salt bridges: F:K.524, F:K.524

8 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.3: 19 residues within 4Å: Chain A: D.609, R.635, R.638 Chain B: D.478, G.480, P.519, P.520, G.521, C.522, G.523, K.524, T.525, L.526, Q.578, I.656, G.684, A.685, T.688 Ligands: MG.5 17 PLIP interactions: 13 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:G.480, B:G.480, B:P.519, B:G.521, B:C.522, B:G.523, B:K.524, B:T.525, B:L.526, B:Q.578, B:T.688 Salt bridges: B:K.524, B:K.524, A:R.635, A:R.635, A:R.635, A:R.638 ATP.6: 21 residues within 4Å: Chain B: D.333, R.359, R.362 Chain C: D.205, I.206, G.207, P.246, P.247, G.248, T.249, G.250, K.251, T.252, L.253, E.305, N.348, I.380, H.384, G.408, A.409 Ligands: MG.9 16 PLIP interactions: 12 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:G.207, C:G.248, C:T.249, C:T.249, C:G.250, C:K.251, C:T.252, C:L.253, C:N.348, C:N.348 Salt bridges: C:K.251, C:K.251, B:R.359, B:R.359, B:R.359, B:R.362 ATP.7: 21 residues within 4Å: Chain B: D.609, R.635, R.638 Chain C: D.478, I.479, G.480, P.520, G.521, C.522, G.523, K.524, T.525, L.526, Q.578, N.624, I.656, N.660, G.684, A.685, T.688 Ligands: MG.8 16 PLIP interactions: 12 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:G.480, C:G.480, C:G.521, C:C.522, C:G.523, C:K.524, C:T.525, C:L.526, C:Q.578, C:N.624 Salt bridges: C:K.524, C:K.524, B:R.635, B:R.635, B:R.635, B:R.638 ATP.10: 20 residues within 4Å: Chain C: D.333, R.359, R.362 Chain D: D.205, I.206, G.207, P.247, G.248, T.249, G.250, K.251, T.252, L.253, E.305, N.348, I.380, H.384, G.408, A.409 Ligands: MG.13 18 PLIP interactions: 14 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:G.207, D:G.207, D:G.248, D:T.249, D:T.249, D:G.250, D:K.251, D:T.252, D:L.253, D:N.348, D:N.348 Salt bridges: D:K.251, D:K.251, D:R.256, C:R.359, C:R.359, C:R.359, C:R.362 ATP.11: 19 residues within 4Å: Chain C: R.635, R.638 Chain D: D.478, I.479, G.480, P.520, G.521, C.522, G.523, K.524, T.525, L.526, Q.578, N.624, I.656, G.684, A.685, T.688 Ligands: MG.12 19 PLIP interactions: 15 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:G.480, D:G.480, D:P.519, D:G.521, D:C.522, D:G.523, D:G.523, D:K.524, D:T.525, D:L.526, D:Q.578, D:N.624, D:T.688 Salt bridges: D:K.524, D:K.524, C:R.635, C:R.635, C:R.635, C:R.638 ATP.14: 20 residues within 4Å: Chain D: D.333, R.359, R.362 Chain E: D.205, I.206, G.207, P.247, G.248, T.249, G.250, K.251, T.252, L.253, R.256, N.348, I.380, H.384, G.408, A.409 Ligands: MG.17 17 PLIP interactions: 13 interactions with chain E, 4 interactions with chain D 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:L.253, E:N.348 Salt bridges: E:K.251, E:K.251, E:R.256, D:R.359, D:R.359, D:R.359, D:R.362 ATP.15: 20 residues within 4Å: Chain D: R.635, R.638 Chain E: D.478, I.479, G.480, P.520, G.521, C.522, G.523, K.524, T.525, L.526, Q.578, N.624, I.656, N.660, G.684, A.685, T.688 Ligands: MG.16 19 PLIP interactions: 15 interactions with chain E, 4 interactions with chain D Hydrogen bonds: E:G.480, E:G.480, E:P.519, E:G.521, E:C.522, E:G.523, E:K.524, E:T.525, E:T.525, E:L.526, E:Q.578, E:N.624, E:T.688 Salt bridges: E:K.524, E:K.524, D:R.635, D:R.635, D:R.635, D:R.638 ATP.18: 18 residues within 4Å: Chain E: F.360 Chain F: D.205, I.206, G.207, P.247, G.248, T.249, G.250, K.251, T.252, L.253, E.305, N.348, I.380, H.384, G.408, A.409 Ligands: MG.20 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:G.207, F:G.207, F:G.248, F:T.249, F:T.249, F:G.250, F:K.251, F:T.252, F:L.253, F:E.305, F:E.305, F:N.348 Salt bridges: F:K.251, F:K.251

8 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 3 residues within 4Å: Chain A: D.609 Chain B: T.525 Ligands: ATP.3 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Chain C: T.525 Ligands: ATP.7 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.525 MG.9: 3 residues within 4Å: Chain C: T.252, D.304 Ligands: ATP.6 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.252 MG.12: 3 residues within 4Å: Chain D: T.525, D.577 Ligands: ATP.11 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.525 MG.13: 3 residues within 4Å: Chain C: R.362 Chain D: T.252 Ligands: ATP.10 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.252 MG.16: 4 residues within 4Å: Chain E: T.525, D.577, Q.578 Ligands: ATP.15 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.525 MG.17: 3 residues within 4Å: Chain D: R.362 Chain E: T.252 Ligands: ATP.14 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.252 MG.20: 3 residues within 4Å: Chain F: T.252, D.304 Ligands: ATP.18 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.252

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pan, M. et al., Mechanistic insight into substrate processing and allosteric inhibition of human p97. Nat.Struct.Mol.Biol. (2021)

Release Date

2021-09-15

Peptides

Transitional endoplasmic reticulum ATPase: ABCDEF
polyubiquitinated Ub-Eos: G

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

Transitional endoplasmic reticulum ATPase

polyubiquitinated Ub-Eos

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