SMTL ID : 5ftj.1

Cryo-EM structure of human p97 bound to UPCDC30245 inhibitor

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.30 Å

Oligo State

homo-hexamer

Ligands

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

ADP.1: 15 residues within 4Å: Chain A: D.205, G.207, G.248, T.249, G.250, K.251, T.252, L.253, I.380, I.383, H.384, G.408, A.409 Chain F: R.359, F.360 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:G.207, 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:T.252, A:L.253, F:R.359 Water bridges: A:T.252, A:G.408 Salt bridges: A:K.251 ADP.2: 14 residues within 4Å: Chain A: D.478, I.479, G.480, G.521, C.522, G.523, K.524, T.525, L.526, I.656, N.660, G.684, A.685, T.688 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:G.480, A:G.480, A:G.521, A:C.522, A:G.523, A:K.524, A:T.525, A:T.525, A:T.525, A:L.526, A:T.688 Salt bridges: A:K.524 ADP.4: 15 residues within 4Å: Chain A: R.359, F.360 Chain B: D.205, G.207, G.248, T.249, G.250, K.251, T.252, L.253, I.380, I.383, H.384, G.408, A.409 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.207, 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, A:R.359 Water bridges: B:T.252, B:G.408 Salt bridges: B:K.251 ADP.5: 14 residues within 4Å: Chain B: D.478, I.479, G.480, G.521, C.522, G.523, K.524, T.525, L.526, I.656, N.660, G.684, A.685, T.688 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:G.480, B:G.480, B:G.521, B:C.522, B:G.523, B:K.524, B:T.525, B:T.525, B:T.525, B:L.526, B:T.688 Salt bridges: B:K.524 ADP.7: 15 residues within 4Å: Chain B: R.359, F.360 Chain C: D.205, G.207, G.248, T.249, G.250, K.251, T.252, L.253, I.380, I.383, H.384, G.408, A.409 15 PLIP interactions: 14 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:G.207, C:G.207, C:G.248, C:T.249, C:T.249, C:G.250, C:K.251, C:T.252, C:T.252, C:T.252, C:L.253, B:R.359 Water bridges: C:T.252, C:G.408 Salt bridges: C:K.251 ADP.8: 14 residues within 4Å: Chain C: D.478, I.479, G.480, G.521, C.522, G.523, K.524, T.525, L.526, I.656, N.660, G.684, A.685, T.688 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:G.480, C:G.480, C:G.521, C:C.522, C:G.523, C:K.524, C:T.525, C:T.525, C:T.525, C:L.526, C:T.688 Salt bridges: C:K.524 ADP.10: 15 residues within 4Å: Chain C: R.359, F.360 Chain D: D.205, G.207, G.248, T.249, G.250, K.251, T.252, L.253, I.380, I.383, H.384, G.408, A.409 15 PLIP interactions: 1 interactions with chain C, 14 interactions with chain D Hydrogen bonds: C:R.359, 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:T.252, D:T.252, D:L.253 Water bridges: D:T.252, D:G.408 Salt bridges: D:K.251 ADP.11: 14 residues within 4Å: Chain D: D.478, I.479, G.480, G.521, C.522, G.523, K.524, T.525, L.526, I.656, N.660, G.684, A.685, T.688 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:G.480, D:G.480, D:G.521, D:C.522, D:G.523, D:K.524, D:T.525, D:T.525, D:T.525, D:L.526, D:T.688 Salt bridges: D:K.524 ADP.13: 15 residues within 4Å: Chain D: R.359, F.360 Chain E: D.205, G.207, G.248, T.249, G.250, K.251, T.252, L.253, I.380, I.383, H.384, G.408, A.409 15 PLIP interactions: 14 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:G.207, E:G.207, E:G.248, E:T.249, E:T.249, E:G.250, E:K.251, E:T.252, E:T.252, E:T.252, E:L.253, D:R.359 Water bridges: E:T.252, E:G.408 Salt bridges: E:K.251 ADP.14: 14 residues within 4Å: Chain E: D.478, I.479, G.480, G.521, C.522, G.523, K.524, T.525, L.526, I.656, N.660, G.684, A.685, T.688 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:G.480, E:G.480, E:G.521, E:C.522, E:G.523, E:K.524, E:T.525, E:T.525, E:T.525, E:L.526, E:T.688 Salt bridges: E:K.524 ADP.16: 15 residues within 4Å: Chain E: R.359, F.360 Chain F: D.205, G.207, G.248, T.249, G.250, K.251, T.252, L.253, I.380, I.383, H.384, G.408, A.409 15 PLIP interactions: 14 interactions with chain F, 1 interactions with chain E 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:T.252, F:T.252, F:L.253, E:R.359 Water bridges: F:T.252, F:G.408 Salt bridges: F:K.251 ADP.17: 14 residues within 4Å: Chain F: D.478, I.479, G.480, G.521, C.522, G.523, K.524, T.525, L.526, I.656, N.660, G.684, A.685, T.688 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:G.480, F:G.480, F:G.521, F:C.522, F:G.523, F:K.524, F:T.525, F:T.525, F:T.525, F:L.526, F:T.688 Salt bridges: F:K.524

6 x OJA: 1-(3-(5-FLUORO-1H-INDOL-2-YL)PHENYL)PIPERIDIN-4-YL)(2-(4-ISOPROPYL-PIPERAZIN1-YL)ETHYL)-CARBAMATE(Non-covalent)

OJA.3: 17 residues within 4Å: Chain A: L.492, V.493, Q.494, P.496, V.497, E.498, P.510, S.511, K.512, C.535, A.537, P.571, C.572, K.614, N.616, V.617, F.618 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.493, A:Q.494, A:P.496, A:P.510, A:A.537, A:P.571, A:K.614, A:K.614, A:F.618 Hydrogen bonds: A:V.493 pi-Stacking: A:F.618, A:F.618 OJA.6: 17 residues within 4Å: Chain B: L.492, V.493, Q.494, P.496, V.497, E.498, P.510, S.511, K.512, C.535, A.537, P.571, C.572, K.614, N.616, V.617, F.618 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:V.493, B:Q.494, B:P.496, B:P.510, B:A.537, B:P.571, B:K.614, B:K.614, B:F.618 Hydrogen bonds: B:V.493 pi-Stacking: B:F.618, B:F.618 OJA.9: 17 residues within 4Å: Chain C: L.492, V.493, Q.494, P.496, V.497, E.498, P.510, S.511, K.512, C.535, A.537, P.571, C.572, K.614, N.616, V.617, F.618 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:V.493, C:Q.494, C:P.496, C:P.510, C:A.537, C:P.571, C:K.614, C:K.614, C:F.618 Hydrogen bonds: C:V.493 pi-Stacking: C:F.618, C:F.618 OJA.12: 17 residues within 4Å: Chain D: L.492, V.493, Q.494, P.496, V.497, E.498, P.510, S.511, K.512, C.535, A.537, P.571, C.572, K.614, N.616, V.617, F.618 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:V.493, D:Q.494, D:P.496, D:P.510, D:A.537, D:P.571, D:K.614, D:K.614, D:F.618 Hydrogen bonds: D:V.493 pi-Stacking: D:F.618, D:F.618 OJA.15: 17 residues within 4Å: Chain E: L.492, V.493, Q.494, P.496, V.497, E.498, P.510, S.511, K.512, C.535, A.537, P.571, C.572, K.614, N.616, V.617, F.618 12 PLIP interactions: 12 interactions with chain E Hydrophobic interactions: E:V.493, E:Q.494, E:P.496, E:P.510, E:A.537, E:P.571, E:K.614, E:K.614, E:F.618 Hydrogen bonds: E:V.493 pi-Stacking: E:F.618, E:F.618 OJA.18: 17 residues within 4Å: Chain F: L.492, V.493, Q.494, P.496, V.497, E.498, P.510, S.511, K.512, C.535, A.537, P.571, C.572, K.614, N.616, V.617, F.618 12 PLIP interactions: 12 interactions with chain F Hydrophobic interactions: F:V.493, F:Q.494, F:P.496, F:P.510, F:A.537, F:P.571, F:K.614, F:K.614, F:F.618 Hydrogen bonds: F:V.493 pi-Stacking: F:F.618, F:F.618

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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