SMTL ID : 6k0r.1 (1 other biounit)

Ruvbl1-Ruvbl2 with truncated domain II in complex with phosphorylated Cordycepin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-3-3-mer

Ligands

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

ADP.1: 18 residues within 4Å: Chain A: S.19, H.20, H.22, G.40, L.41, V.42, Q.44, P.73, G.75, T.76, G.77, K.78, T.79, A.80, Y.265, I.273, L.302, R.303 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:S.19, A:H.20, A:V.42, A:G.75, A:T.76, A:G.77, A:K.78, A:T.79, A:T.79, A:T.79, A:A.80, A:Y.265, A:Y.265 Salt bridges: A:H.20, A:K.78, A:R.303, A:R.303

4 x CUU: [(2~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-oxolan-2-yl]methyl phosphono hydrogen phosphate(Non-covalent)

CUU.2: 17 residues within 4Å: Chain B: S.19, H.20, H.22, V.23, G.40, L.41, V.42, P.74, G.75, T.76, G.77, K.78, T.79, A.80, Y.265, I.273, L.302 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:H.20, B:V.42, B:G.75, B:T.76, B:G.77, B:K.78, B:T.79, B:A.80, B:Y.265, B:Y.265 Salt bridges: B:H.20, B:K.78 CUU.3: 18 residues within 4Å: Chain C: S.19, H.20, H.22, G.40, L.41, V.42, P.73, P.74, G.75, T.76, G.77, K.78, T.79, A.80, D.201, Y.265, I.273, L.302 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:H.20, C:V.42, C:G.75, C:T.76, C:G.77, C:K.78, C:T.79, C:T.79, C:T.79, C:A.80, C:Y.265, C:Y.265 Salt bridges: C:H.20, C:K.78 CUU.4: 16 residues within 4Å: Chain D: H.28, H.30, I.31, M.49, V.50, G.83, T.84, G.85, K.86, T.87, A.88, Y.265, I.273, L.302, I.306 Ligands: MG.5 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:H.28, D:V.50, D:G.83, D:T.84, D:G.85, D:K.86, D:T.87, D:T.87, D:T.87, D:A.88, D:Y.265, D:Y.265 Salt bridges: D:H.28, D:K.86 CUU.7: 19 residues within 4Å: Chain F: A.27, H.28, H.30, I.31, G.48, M.49, V.50, Q.52, Q.81, G.83, T.84, G.85, K.86, T.87, A.88, Y.265, I.273, L.302, I.306 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:H.28, F:V.50, F:G.83, F:T.84, F:G.85, F:K.86, F:T.87, F:T.87, F:T.87, F:A.88, F:Y.265, F:Y.265 Salt bridges: F:H.28, F:K.86

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 2 residues within 4Å: Chain C: D.255 Ligands: CUU.4 No protein-ligand interaction detected (PLIP)

1 x 3AT: 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

3AT.6: 19 residues within 4Å: Chain A: D.255 Chain E: A.27, H.30, I.31, G.48, M.49, V.50, P.82, G.83, T.84, G.85, K.86, T.87, A.88, D.202, Y.265, I.273, L.302, I.306 16 PLIP interactions: 14 interactions with chain E, 2 interactions with chain A Hydrogen bonds: E:A.27, E:V.50, E:G.83, E:T.84, E:G.85, E:G.85, E:K.86, E:T.87, E:T.87, E:A.88, E:Y.265, E:Y.265, A:D.255, A:D.255 Salt bridges: E:K.86, E:K.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ju, D. et al., Chemical perturbations reveal that RUVBL2 regulates the circadian phase in mammals. Sci Transl Med (2020)

Release Date

2020-05-06

Peptides

RuvB-like 1,RuvB-like 1: ABC
RuvB-like 2,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 1

RuvB-like 2,RuvB-like 2

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