SMTL ID : 8efv.1

Structure of single homo-hexameric Holliday junction ATP-dependent DNA helicase RuvB motor

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

3 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.1: 14 residues within 4Å: Chain A: R.7, P.8, Y.14, I.15, P.47, G.48, L.49, G.50, K.51, T.52, T.53, Y.168, R.205 Chain B: R.158 12 PLIP interactions: 10 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.7, A:R.7, A:I.15, A:G.48, A:G.48, A:G.50, A:K.51, A:Y.168, A:Y.168, B:R.158, B:R.158 Salt bridges: A:R.205 AGS.3: 20 residues within 4Å: Chain B: A.5, L.6, R.7, P.8, Y.14, I.15, P.47, G.48, L.49, G.50, K.51, T.52, T.53, T.146, Y.168, M.204, R.205, K.208 Chain C: E.115, R.158 21 PLIP interactions: 18 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:I.15, B:G.48, B:L.49, B:G.50, B:K.51, B:T.52, B:T.52, B:T.53, B:T.53, B:Y.168, B:Y.168, B:R.205, B:R.205, B:K.208, C:E.115, C:R.158, C:R.158 Salt bridges: B:R.7, B:K.51, B:R.205, B:R.205 AGS.5: 22 residues within 4Å: Chain C: A.5, L.6, R.7, P.8, Y.14, I.15, P.47, G.48, L.49, G.50, K.51, T.52, T.53, T.146, Y.168, M.204, R.205, K.208 Chain D: E.115, P.154, R.158 Ligands: MG.6 20 PLIP interactions: 18 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:I.15, C:G.48, C:L.49, C:G.50, C:K.51, C:K.51, C:T.52, C:T.52, C:T.53, C:T.53, C:Y.168, C:Y.168, C:R.205, C:R.205, D:R.158, D:R.158 Salt bridges: C:R.7, C:K.51, C:R.205, C:R.205

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: E.98 Chain B: P.154 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.98 MG.4: 3 residues within 4Å: Chain B: E.98, H.100, T.146 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:T.146 MG.6: 2 residues within 4Å: Chain C: E.98 Ligands: AGS.5 No protein-ligand interaction detected (PLIP) MG.8: 5 residues within 4Å: Chain D: K.51, D.97, E.98, A.144 Ligands: ADP.7 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.97, D:D.97

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

ADP.7: 17 residues within 4Å: Chain D: A.5, L.6, R.7, P.8, Y.14, I.15, G.48, L.49, G.50, K.51, T.52, T.53, Y.168, M.204, R.205, K.208 Ligands: MG.8 18 PLIP interactions: 18 interactions with chain D Hydrogen bonds: D:A.5, D:A.5, D:I.15, D:G.48, D:L.49, D:G.50, D:K.51, D:T.52, D:T.52, D:T.52, D:T.53, D:Y.168, D:Y.168, D:K.208 Salt bridges: D:R.7, D:K.51, D:R.205, D:R.205 ADP.9: 16 residues within 4Å: Chain E: R.7, P.8, Y.14, I.15, G.48, L.49, G.50, K.51, T.52, T.53, D.97, Y.168, R.179, M.204, R.205, K.208 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:I.15, E:G.48, E:G.50, E:K.51, E:T.52, E:T.52, E:D.97, E:Y.168, E:R.179, E:R.205 Salt bridges: E:R.205 ADP.10: 16 residues within 4Å: Chain F: L.6, R.7, P.8, Y.14, I.15, G.48, L.49, G.50, K.51, T.52, T.53, Y.168, R.179, M.204, R.205, K.208 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:L.6, F:I.15, F:G.48, F:L.49, F:G.50, F:K.51, F:T.52, F:T.52, F:Y.168, F:R.205 Salt bridges: F:R.205

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shen, Z.F. et al., Structure of single homo-hexameric Holliday junction ATP-dependent DNA helicase RuvB motor. To Be Published

Release Date

2023-05-10

Peptides

Holliday junction ATP-dependent DNA helicase RuvB: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
C

C
B

D
A

E
F

F
E

Holliday junction ATP-dependent DNA helicase RuvB

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