SMTL ID : 7lmy.1

Cryo-EM structure of human p97 in complex with NMS-873 in the presence of ATP, Npl4/Ufd1, and Ub6

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

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

ATP.1: 17 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, G.408, A.409 Chain F: R.359, F.360 Ligands: MG.4 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:L.253, A:N.348 Salt bridges: A:K.251, A:K.251 ATP.2: 18 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, I.656, N.660, G.684, A.685, T.688 Chain F: R.635 Ligands: MG.5 14 PLIP interactions: 13 interactions with chain A, 1 interactions with chain F Hydrogen bonds: 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:T.525, A:L.526, A:N.624 Salt bridges: A:K.524, A:K.524, F:R.635 ATP.6: 17 residues within 4Å: Chain A: R.359, F.360 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, G.408, A.409 Ligands: MG.9 11 PLIP interactions: 11 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:L.253, B:N.348 Salt bridges: B:K.251, B:K.251 ATP.7: 18 residues within 4Å: Chain A: R.635 Chain B: D.478, I.479, G.480, P.520, G.521, C.522, G.523, K.524, T.525, L.526, N.624, I.656, N.660, G.684, A.685, T.688 Ligands: MG.10 14 PLIP interactions: 13 interactions with chain B, 1 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:T.525, B:L.526, B:N.624 Salt bridges: B:K.524, B:K.524, A:R.635 ATP.11: 17 residues within 4Å: Chain B: R.359, F.360 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, G.408, A.409 Ligands: MG.14 11 PLIP interactions: 11 interactions with chain C 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 Salt bridges: C:K.251, C:K.251 ATP.12: 18 residues within 4Å: Chain B: R.635 Chain C: D.478, I.479, G.480, P.520, G.521, C.522, G.523, K.524, T.525, L.526, N.624, I.656, N.660, G.684, A.685, T.688 Ligands: MG.15 14 PLIP interactions: 13 interactions with chain C, 1 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:T.525, C:L.526, C:N.624 Salt bridges: C:K.524, C:K.524, B:R.635 ATP.16: 17 residues within 4Å: Chain C: R.359, F.360 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, G.408, A.409 Ligands: MG.19 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:L.253, D:N.348 Salt bridges: D:K.251, D:K.251 ATP.17: 18 residues within 4Å: Chain C: R.635 Chain D: D.478, I.479, G.480, P.520, G.521, C.522, G.523, K.524, T.525, L.526, N.624, I.656, N.660, G.684, A.685, T.688 Ligands: MG.20 14 PLIP interactions: 13 interactions with chain D, 1 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:T.525, D:L.526, D:N.624 Salt bridges: D:K.524, D:K.524, C:R.635 ATP.21: 17 residues within 4Å: Chain D: R.359, F.360 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, G.408, A.409 Ligands: MG.24 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:G.207, E:G.248, 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 ATP.22: 18 residues within 4Å: Chain D: R.635 Chain E: D.478, I.479, G.480, P.520, G.521, C.522, G.523, K.524, T.525, L.526, N.624, I.656, N.660, G.684, A.685, T.688 Ligands: MG.25 14 PLIP interactions: 13 interactions with chain E, 1 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:T.525, E:L.526, E:N.624 Salt bridges: E:K.524, E:K.524, D:R.635 ATP.26: 17 residues within 4Å: Chain E: 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, G.408, A.409 Ligands: MG.29 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: 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:N.348 Salt bridges: F:K.251, F:K.251 ATP.27: 18 residues within 4Å: Chain E: R.635 Chain F: D.478, I.479, G.480, P.520, G.521, C.522, G.523, K.524, T.525, L.526, N.624, I.656, N.660, G.684, A.685, T.688 Ligands: MG.30 14 PLIP interactions: 13 interactions with chain F, 1 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:T.525, F:L.526, F:N.624 Salt bridges: F:K.524, F:K.524, E:R.635

6 x Y6Y: 3-[3-cyclopentylsulfanyl-5-[[3-methyl-4-(4-methylsulfonylphenyl)phenoxy]methyl]-1,2,4-triazol-4-yl]pyridine(Non-covalent)

Y6Y.3: 19 residues within 4Å: Chain A: L.492, V.493, P.496, V.497, P.500, L.504, G.507, M.508, T.509, P.510, S.511, K.512, C.535, A.537, C.572, V.573, K.615, N.616, F.618 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.493, A:P.500, A:K.512, A:A.537, A:V.573, A:K.615, A:F.618 pi-Cation interactions: A:K.615 Y6Y.8: 19 residues within 4Å: Chain B: L.492, V.493, P.496, V.497, P.500, L.504, G.507, M.508, T.509, P.510, S.511, K.512, C.535, A.537, C.572, V.573, K.615, N.616, F.618 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.493, B:P.500, B:K.512, B:A.537, B:V.573, B:K.615, B:F.618 pi-Cation interactions: B:K.615 Y6Y.13: 19 residues within 4Å: Chain C: L.492, V.493, P.496, V.497, P.500, L.504, G.507, M.508, T.509, P.510, S.511, K.512, C.535, A.537, C.572, V.573, K.615, N.616, F.618 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:V.493, C:P.500, C:K.512, C:A.537, C:V.573, C:K.615, C:F.618 pi-Cation interactions: C:K.615 Y6Y.18: 19 residues within 4Å: Chain D: L.492, V.493, P.496, V.497, P.500, L.504, G.507, M.508, T.509, P.510, S.511, K.512, C.535, A.537, C.572, V.573, K.615, N.616, F.618 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:V.493, D:P.500, D:K.512, D:A.537, D:V.573, D:K.615, D:F.618 pi-Cation interactions: D:K.615 Y6Y.23: 19 residues within 4Å: Chain E: L.492, V.493, P.496, V.497, P.500, L.504, G.507, M.508, T.509, P.510, S.511, K.512, C.535, A.537, C.572, V.573, K.615, N.616, F.618 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:V.493, E:P.500, E:K.512, E:A.537, E:V.573, E:K.615, E:F.618 pi-Cation interactions: E:K.615 Y6Y.28: 19 residues within 4Å: Chain F: L.492, V.493, P.496, V.497, P.500, L.504, G.507, M.508, T.509, P.510, S.511, K.512, C.535, A.537, C.572, V.573, K.615, N.616, F.618 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:V.493, F:P.500, F:K.512, F:A.537, F:V.573, F:K.615, F:F.618 pi-Cation interactions: F:K.615

12 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: T.252, D.304 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.252 MG.5: 4 residues within 4Å: Chain A: T.525, D.577 Chain F: R.635 Ligands: ATP.2 No protein-ligand interaction detected (PLIP) MG.9: 3 residues within 4Å: Chain B: T.252, D.304 Ligands: ATP.6 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.252 MG.10: 4 residues within 4Å: Chain A: R.635 Chain B: T.525, D.577 Ligands: ATP.7 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain C: T.252, D.304 Ligands: ATP.11 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.252 MG.15: 4 residues within 4Å: Chain B: R.635 Chain C: T.525, D.577 Ligands: ATP.12 No protein-ligand interaction detected (PLIP) MG.19: 3 residues within 4Å: Chain D: T.252, D.304 Ligands: ATP.16 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.252 MG.20: 4 residues within 4Å: Chain C: R.635 Chain D: T.525, D.577 Ligands: ATP.17 No protein-ligand interaction detected (PLIP) MG.24: 3 residues within 4Å: Chain E: T.252, D.304 Ligands: ATP.21 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.252 MG.25: 4 residues within 4Å: Chain D: R.635 Chain E: T.525, D.577 Ligands: ATP.22 No protein-ligand interaction detected (PLIP) MG.29: 3 residues within 4Å: Chain F: T.252, D.304 Ligands: ATP.26 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.252 MG.30: 4 residues within 4Å: Chain E: R.635 Chain F: T.525, D.577 Ligands: ATP.27 No protein-ligand interaction detected (PLIP)

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

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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