SMTL ID : 9emc.1

RUVBL1/2 in complex with ATP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

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

ATP.1: 23 residues within 4Å: Chain A: S.20, H.21, H.23, G.41, L.42, V.43, P.74, P.75, G.76, T.77, G.78, K.79, T.80, A.81, E.306, N.335, Y.369, I.377, R.407 Chain E: E.335, D.367, R.371 Ligands: MG.2 21 PLIP interactions: 19 interactions with chain A, 2 interactions with chain E Hydrogen bonds: A:S.20, A:H.21, A:V.43, A:P.74, A:G.76, A:T.77, A:G.78, A:K.79, A:T.80, A:T.80, A:T.80, A:A.81, A:Y.369, E:D.367 Salt bridges: A:H.21, A:K.79, A:K.79, A:R.407, A:R.407, A:R.407, E:R.371 ATP.3: 22 residues within 4Å: Chain A: E.323, R.360 Chain B: A.42, H.43, H.45, G.63, M.64, V.65, Q.96, P.97, G.98, T.99, G.100, K.101, T.102, A.103, N.347, Y.380, I.388, L.417, R.418 Ligands: MG.4 20 PLIP interactions: 18 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:A.42, B:H.43, B:V.65, B:Q.96, B:G.98, B:T.99, B:G.100, B:K.101, B:T.102, B:A.103, B:Y.380, B:Y.380, A:E.323 Salt bridges: B:H.43, B:K.101, B:K.101, B:R.418, B:R.418, B:R.418, A:R.360 ATP.5: 23 residues within 4Å: Chain B: E.335, D.367, R.371 Chain C: S.20, H.21, H.23, G.41, L.42, V.43, P.74, P.75, G.76, T.77, G.78, K.79, T.80, A.81, E.306, N.335, Y.369, I.377, R.407 Ligands: MG.6 21 PLIP interactions: 2 interactions with chain B, 19 interactions with chain C Hydrogen bonds: B:D.367, C:S.20, C:H.21, C:V.43, C:P.74, C:G.76, C:T.77, C:G.78, C:K.79, C:T.80, C:T.80, C:T.80, C:A.81, C:Y.369 Salt bridges: B:R.371, C:H.21, C:K.79, C:K.79, C:R.407, C:R.407, C:R.407 ATP.7: 23 residues within 4Å: Chain D: S.20, H.21, H.23, G.41, L.42, V.43, P.74, P.75, G.76, T.77, G.78, K.79, T.80, A.81, E.306, N.335, Y.369, I.377, R.407 Chain F: E.335, D.367, R.371 Ligands: MG.8 21 PLIP interactions: 19 interactions with chain D, 2 interactions with chain F Hydrogen bonds: D:S.20, D:H.21, D:V.43, D:P.74, D:G.76, D:T.77, D:G.78, D:K.79, D:T.80, D:T.80, D:T.80, D:A.81, D:Y.369, F:D.367 Salt bridges: D:H.21, D:K.79, D:K.79, D:R.407, D:R.407, D:R.407, F:R.371 ATP.9: 22 residues within 4Å: Chain D: E.323, R.360 Chain E: A.42, H.43, H.45, G.63, M.64, V.65, Q.96, P.97, G.98, T.99, G.100, K.101, T.102, A.103, N.347, Y.380, I.388, L.417, R.418 Ligands: MG.10 20 PLIP interactions: 18 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:A.42, E:H.43, E:V.65, E:Q.96, E:G.98, E:T.99, E:G.100, E:K.101, E:T.102, E:A.103, E:Y.380, E:Y.380, D:E.323 Salt bridges: E:H.43, E:K.101, E:K.101, E:R.418, E:R.418, E:R.418, D:R.360 ATP.11: 22 residues within 4Å: Chain C: E.323, R.360 Chain F: A.42, H.43, H.45, G.63, M.64, V.65, Q.96, P.97, G.98, T.99, G.100, K.101, T.102, A.103, N.347, Y.380, I.388, L.417, R.418 Ligands: MG.12 20 PLIP interactions: 18 interactions with chain F, 2 interactions with chain C Hydrogen bonds: F:A.42, F:H.43, F:V.65, F:Q.96, F:G.98, F:T.99, F:G.100, F:K.101, F:T.102, F:A.103, F:Y.380, F:Y.380, C:E.323 Salt bridges: F:H.43, F:K.101, F:K.101, F:R.418, F:R.418, F:R.418, C:R.360

6 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: T.80, D.305 Chain E: E.335, R.371 Ligands: ATP.1 No protein-ligand interaction detected (PLIP) MG.4: 5 residues within 4Å: Chain A: E.323, R.360 Chain B: T.102, D.317 Ligands: ATP.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.102 MG.6: 5 residues within 4Å: Chain B: E.335, R.371 Chain C: T.80, D.305 Ligands: ATP.5 No protein-ligand interaction detected (PLIP) MG.8: 5 residues within 4Å: Chain D: T.80, D.305 Chain F: E.335, R.371 Ligands: ATP.7 No protein-ligand interaction detected (PLIP) MG.10: 5 residues within 4Å: Chain D: E.323, R.360 Chain E: T.102, D.317 Ligands: ATP.9 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.102 MG.12: 5 residues within 4Å: Chain C: E.323, R.360 Chain F: T.102, D.317 Ligands: ATP.11 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:T.102

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Garcia-Martin, C. et al., Mechanism of allosteric inhibition of RUVBL1-RUVBL2 by the small-molecule CB-6644. Cell Rep Phys Sci (2024)

Release Date

2024-05-15

Peptides

RuvB-like 1: ACD
RuvB-like 2: BEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
B

D
C

B
D

E
F

F
E

RuvB-like 1

RuvB-like 2

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