SMTL ID : 9ema.1

RUVBL1/2 in complex with ATP and CB-6644 inhibitor

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

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

ATP.1: 22 residues within 4Å: Chain A: S.20, H.21, H.23, G.41, L.42, V.43, P.75, G.76, T.77, G.78, K.79, T.80, A.81, D.305, E.306, N.335, Y.369, I.377, R.407 Chain F: E.335, R.371 Ligands: MG.11 19 PLIP interactions: 1 interactions with chain F, 18 interactions with chain A Salt bridges: F:R.371, A:H.21, A:K.79, A:K.79, A:R.407, A:R.407 Hydrogen bonds: A:H.21, A:V.43, A:G.76, A:T.77, A:G.78, A:K.79, A:T.80, A:T.80, A:A.81, A:E.306, A:N.335, A:Y.369, A:Y.369 ATP.3: 21 residues within 4Å: Chain B: S.20, H.21, H.23, G.41, L.42, V.43, P.75, G.76, T.77, G.78, K.79, T.80, A.81, D.305, E.306, Y.369, I.377, L.406, R.407 Chain D: E.335, R.371 22 PLIP interactions: 21 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:H.21, B:V.43, B:G.76, B:T.77, B:G.78, B:K.79, B:T.80, B:T.80, B:T.80, B:A.81, B:E.306, B:E.306, B:E.306, B:Y.369, B:Y.369 Salt bridges: B:H.21, B:K.79, B:K.79, B:R.407, B:R.407, B:R.407, D:R.371 ATP.5: 19 residues within 4Å: Chain C: S.20, H.21, H.23, G.41, L.42, V.43, P.75, G.76, T.77, G.78, K.79, T.80, A.81, D.305, Y.369, I.377, R.407 Chain E: E.335, R.371 20 PLIP interactions: 18 interactions with chain C, 2 interactions with chain E Hydrogen bonds: C:H.21, C:V.43, C:G.76, C:T.77, C:G.78, C:K.79, C:T.80, C:T.80, C:A.81, C:D.305, C:Y.369, C:Y.369, E:E.335 Salt bridges: C:H.21, C:K.79, C:K.79, C:R.407, C:R.407, C:R.407, E:R.371 ATP.7: 24 residues within 4Å: Chain A: E.323, R.360 Chain D: 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, E.318, N.347, Y.380, I.388, L.417, R.418, I.421 Ligands: MG.8 18 PLIP interactions: 17 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:H.43, D:V.65, D:G.98, D:T.99, D:G.100, D:K.101, D:T.102, D:A.103, D:N.347, D:Y.380, D:Y.380 Salt bridges: D:H.43, D:K.101, D:K.101, D:R.418, D:R.418, D:R.418, A:R.360 ATP.9: 25 residues within 4Å: Chain B: E.323, R.360 Chain E: A.42, H.43, H.45, I.46, G.63, M.64, V.65, Q.96, P.97, G.98, T.99, G.100, K.101, T.102, A.103, E.318, N.347, Y.380, I.388, L.417, R.418, I.421 Ligands: MG.10 18 PLIP interactions: 17 interactions with chain E, 1 interactions with chain B Hydrogen bonds: E:H.43, E:V.65, E:G.98, E:T.99, E:G.100, E:K.101, E:T.102, E:A.103, E:N.347, E:Y.380, E:Y.380 Salt bridges: E:H.43, E:K.101, E:K.101, E:R.418, E:R.418, E:R.418, B:R.360 ATP.12: 25 residues within 4Å: Chain C: E.323, R.360 Chain F: A.42, H.43, H.45, I.46, G.63, M.64, V.65, Q.96, P.97, G.98, T.99, G.100, K.101, T.102, A.103, E.318, N.347, Y.380, I.388, L.417, R.418, I.421 Ligands: MG.13 18 PLIP interactions: 1 interactions with chain C, 17 interactions with chain F Salt bridges: C:R.360, F:H.43, F:K.101, F:K.101, F:R.418, F:R.418, F:R.418 Hydrogen bonds: F:H.43, F:V.65, F:G.98, F:T.99, F:G.100, F:K.101, F:T.102, F:A.103, F:N.347, F:Y.380, F:Y.380

3 x 01: 5-chloranyl-2-ethoxy-4-fluoranyl-~{N}-[4-[[3-(methoxymethyl)-1-oxidanylidene-6,7-dihydro-5~{H}-pyrazolo[1,2-a][1,2]benzodiazepin-2-yl]amino]-2,2-dimethyl-4-oxidanylidene-butyl]benzamide

01.2: 21 residues within 4Å: Chain A: M.116, F.119, R.120, I.123, D.276, R.279, G.280, N.283, R.320, A.321, S.324, I.326, A.327, P.328 Chain D: T.102, A.105, M.106, A.109, F.118, A.120, F.315 12 PLIP interactions: 7 interactions with chain A, 5 interactions with chain D Hydrophobic interactions: A:R.279, A:I.326, D:T.102, D:M.106, D:A.109, D:F.118, D:F.315 Hydrogen bonds: A:R.120, A:N.283, A:R.320, A:S.324 Halogen bonds: A:F.119 01.4: 21 residues within 4Å: Chain B: M.116, F.119, R.120, I.123, D.276, R.279, G.280, N.283, R.320, A.321, S.324, I.326, A.327, P.328 Chain E: T.102, A.105, M.106, A.109, F.118, A.120, F.315 14 PLIP interactions: 8 interactions with chain B, 6 interactions with chain E Hydrophobic interactions: B:R.279, B:I.326, E:T.102, E:M.106, E:A.109, E:F.118, E:F.118, E:F.315 Hydrogen bonds: B:R.120, B:N.283, B:R.320, B:S.324, B:S.324 Halogen bonds: B:F.119 01.6: 20 residues within 4Å: Chain C: M.116, F.119, R.120, I.123, D.276, R.279, G.280, N.283, R.320, A.321, S.324, I.326, A.327 Chain F: T.102, A.105, M.106, A.109, F.118, A.120, F.315 14 PLIP interactions: 7 interactions with chain C, 7 interactions with chain F Hydrophobic interactions: C:R.279, C:I.326, F:T.102, F:A.105, F:A.109, F:F.118, F:F.118, F:A.120, F:F.315 Hydrogen bonds: C:R.120, C:N.283, C:R.320, C:S.324 Halogen bonds: C:F.119

4 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 4 residues within 4Å: Chain D: T.102, D.317, E.318 Ligands: ATP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.102 MG.10: 4 residues within 4Å: Chain B: R.360 Chain E: T.102, E.318 Ligands: ATP.9 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:T.102 MG.11: 6 residues within 4Å: Chain A: H.21, T.80, R.407 Chain F: E.335, R.371 Ligands: ATP.1 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:E.335 MG.13: 4 residues within 4Å: Chain C: E.323, R.360 Chain F: T.102 Ligands: ATP.12 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: ABC
RuvB-like 2: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

RuvB-like 1

RuvB-like 2

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