SMTL ID : 8efy.1

Structure of double homo-hexameric AAA+ ATPase RuvB motors

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-12-mer

Ligands

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

ADP.1: 14 residues within 4Å: Chain A: 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 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:I.15, A:G.48, A:G.50, A:K.51, A:T.52, A:T.52, A:T.52, A:T.53, A:Y.168 Salt bridges: A:R.7, A:K.51 ADP.9: 16 residues within 4Å: Chain E: L.6, R.7, P.8, Y.14, I.15, P.47, G.48, L.49, G.50, K.51, T.52, T.53, Y.168, M.204, R.205, K.208 11 PLIP interactions: 11 interactions with chain E Hydrogen bonds: E:L.6, E:R.7, E:I.15, E:G.48, E:G.48, E:G.50, E:K.51, E:T.52, E:Y.168 Salt bridges: E:R.205, E:R.205 ADP.10: 14 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, M.204, R.205 10 PLIP interactions: 10 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 Salt bridges: F:R.205 ADP.11: 17 residues within 4Å: Chain I: 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.12 18 PLIP interactions: 18 interactions with chain I Hydrogen bonds: I:A.5, I:L.6, I:R.7, I:I.15, I:G.48, I:G.50, I:K.51, I:T.52, I:T.52, I:T.53, I:T.53, I:Y.168, I:Y.168, I:K.208 Salt bridges: I:R.7, I:K.51, I:R.205, I:R.205 ADP.19: 15 residues within 4Å: Chain M: L.6, R.7, P.8, Y.14, I.15, P.47, G.48, L.49, G.50, K.51, T.53, Y.168, M.204, R.205, K.208 11 PLIP interactions: 11 interactions with chain M Hydrogen bonds: M:L.6, M:R.7, M:I.15, M:G.48, M:G.48, M:G.50, M:K.51, M:T.52, M:Y.168 Salt bridges: M:R.205, M:R.205 ADP.20: 14 residues within 4Å: Chain N: 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 10 PLIP interactions: 10 interactions with chain N Hydrogen bonds: N:I.15, N:G.48, N:L.49, N:G.50, N:K.51, N:T.52, N:T.52, N:Y.168, N:R.205 Salt bridges: N:R.205

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.97, E.98, A.144 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.97, A:D.97, A:E.98 MG.4: 2 residues within 4Å: Chain B: E.98 Ligands: AGS.3 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.98 MG.6: 3 residues within 4Å: Chain C: E.98, H.100, T.146 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.98 MG.8: 1 residues within 4Å: Chain D: E.98 No protein-ligand interaction detected (PLIP) MG.12: 5 residues within 4Å: Chain I: T.52, D.97, E.98, A.144 Ligands: ADP.11 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:D.97, I:D.97 MG.14: 2 residues within 4Å: Chain J: E.98 Ligands: AGS.13 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:E.98 MG.16: 3 residues within 4Å: Chain K: E.98, H.100, T.146 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:E.98, K:T.146 MG.18: 2 residues within 4Å: Chain L: P.47 Ligands: AGS.17 No protein-ligand interaction detected (PLIP)

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

AGS.3: 20 residues within 4Å: Chain A: E.115, R.158 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, Y.168, M.204, R.205, K.208 Ligands: MG.4 20 PLIP interactions: 17 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:I.15, B:G.48, B:L.49, B:G.50, B:K.51, B:K.51, B:T.52, B:T.52, B:T.53, B:Y.168, B:Y.168, B:R.205, B:R.205, A:E.115, A:R.158, A:R.158 Salt bridges: B:R.7, B:K.51, B:R.205, B:R.205 AGS.5: 19 residues within 4Å: Chain B: E.115, R.158 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, Y.168, M.204, R.205, K.208 20 PLIP interactions: 20 interactions with chain C Hydrogen bonds: C:L.6, C:R.7, C:I.15, C:G.16, C:G.48, C:L.49, C:G.50, C:K.51, C:T.52, C:T.52, C:T.53, C:Y.168, C:Y.168, C:R.205, C:R.205, C:K.208 Salt bridges: C:R.7, C:K.51, C:R.205, C:R.205 AGS.7: 14 residues within 4Å: Chain C: R.158 Chain D: R.7, P.8, Y.14, I.15, P.47, G.48, L.49, G.50, K.51, T.52, T.53, Y.168, M.204 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:R.7, D:I.15, D:L.49, D:G.50, D:K.51, D:T.52, D:Y.168, D:Y.168 Salt bridges: D:K.51 AGS.13: 21 residues within 4Å: Chain I: E.115, P.154, R.158 Chain J: 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, Y.168, M.204, R.205, K.208 Ligands: MG.14 21 PLIP interactions: 19 interactions with chain J, 2 interactions with chain I Hydrogen bonds: J:L.4, J:I.15, J:G.48, J:L.49, J:G.50, J:K.51, J:K.51, J:T.52, J:T.52, J:T.53, J:Y.168, J:Y.168, J:R.205, J:R.205, J:K.208, I:R.158, I:R.158 Salt bridges: J:R.7, J:K.51, J:R.205, J:R.205 AGS.15: 19 residues within 4Å: Chain J: E.115, R.158 Chain K: 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, Y.168, M.204, R.205, K.208 17 PLIP interactions: 17 interactions with chain K Hydrogen bonds: K:L.6, K:I.15, K:L.49, K:G.50, K:K.51, K:T.52, K:T.52, K:T.53, K:Y.168, K:Y.168, K:R.205, K:R.205, K:K.208 Salt bridges: K:R.7, K:K.51, K:R.205, K:R.205 AGS.17: 13 residues within 4Å: Chain K: R.158 Chain L: P.8, Y.14, I.15, P.47, G.48, L.49, G.50, K.51, T.52, T.53, Y.168 Ligands: MG.18 7 PLIP interactions: 7 interactions with chain L Hydrogen bonds: L:I.15, L:L.49, L:K.51, L:T.52, L:Y.168, L:Y.168 Salt bridges: L:K.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rish, A.D. et al., Structure of double homo-hexameric AAA+ ATPase RuvB motor binding with DNA substrate. To Be Published

Release Date

2023-05-10

Peptides

Holliday junction ATP-dependent DNA helicase RuvB: ABCDEFIJKLMN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

I
I

J
J

K
K

L
L

M
M

N
N

Holliday junction ATP-dependent DNA helicase RuvB

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