SMTL ID : 6qel.1

E. coli DnaBC apo complex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-6-mer

Ligands

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

ADP.1: 15 residues within 4Å: Chain A: P.233, S.234, M.235, G.236, K.237, T.238, T.239, E.262, R.271, R.420, F.453, G.455, Q.456, S.458 Ligands: MG.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.236, A:K.237, A:T.238, A:T.238, A:T.239, A:R.420, A:R.420 Salt bridges: A:K.237 ADP.3: 22 residues within 4Å: Chain A: K.440, Q.441, R.442, N.443, G.444, P.445 Chain B: P.233, S.234, M.235, G.236, K.237, T.238, T.239, E.262, R.271, Q.281, T.282, R.420, F.453, G.455, Q.456 Ligands: MG.4 11 PLIP interactions: 8 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.234, B:G.236, B:K.237, B:T.238, B:E.262, B:Q.281 Salt bridges: B:K.237, B:R.271, A:K.440, A:R.442, A:R.442 ADP.5: 22 residues within 4Å: Chain B: K.440, Q.441, R.442, N.443, G.444, P.445 Chain C: P.233, S.234, G.236, K.237, T.238, T.239, E.262, R.271, Q.281, T.282, R.420, F.453, G.455, Q.456, S.458 Ligands: MG.6 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain C Hydrogen bonds: B:Q.441, C:G.236, C:K.237, C:T.238, C:Q.281 Salt bridges: B:K.440, B:R.442, C:K.237, C:R.271 ADP.7: 23 residues within 4Å: Chain C: K.440, Q.441, R.442, N.443, G.444, P.445 Chain D: P.233, S.234, G.236, K.237, T.238, T.239, E.262, R.271, Q.281, T.282, Q.384, R.420, F.453, G.455, Q.456, S.458 Ligands: MG.8 9 PLIP interactions: 3 interactions with chain C, 6 interactions with chain D Hydrogen bonds: C:Q.441, C:R.442, D:T.238, D:T.239, D:Q.281, D:R.420 Salt bridges: C:R.442, D:K.237, D:R.271 ADP.9: 22 residues within 4Å: Chain D: K.440, Q.441, R.442, N.443, G.444, P.445 Chain E: P.233, S.234, G.236, K.237, T.238, T.239, E.262, R.271, Q.281, T.282, R.420, F.453, G.455, Q.456, S.458 Ligands: MG.10 12 PLIP interactions: 8 interactions with chain E, 4 interactions with chain D Hydrogen bonds: E:G.236, E:K.237, E:T.238, E:T.239, E:E.262, E:R.271, E:Q.384, D:R.442, D:N.443 Salt bridges: E:K.237, D:K.440, D:R.442 ADP.11: 24 residues within 4Å: Chain E: K.440, Q.441, R.442, N.443, G.444, P.445, I.446 Chain F: P.233, S.234, M.235, G.236, K.237, T.238, T.239, E.262, R.271, Q.281, T.282, R.420, F.453, G.455, Q.456, S.458 Ligands: MG.12 6 PLIP interactions: 5 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:G.236, F:T.238, F:T.239, F:Q.281, E:R.442 Salt bridges: F:K.237 ADP.13: 13 residues within 4Å: Chain G: L.65, H.66, Y.74, R.75, P.108, G.109, T.110, G.111, K.112, N.113, H.114, W.233 Ligands: MG.14 12 PLIP interactions: 12 interactions with chain G Hydrogen bonds: G:R.75, G:R.75, G:G.109, G:T.110, G:G.111, G:K.112, G:N.113, G:N.113, G:H.114, G:H.114 Salt bridges: G:H.66, G:K.112

12 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: T.238, E.262, D.343 Ligands: ADP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.238, A:E.262 MG.4: 4 residues within 4Å: Chain A: R.442 Chain B: T.238, E.262 Ligands: ADP.3 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:T.238, B:E.262, B:E.262 MG.6: 5 residues within 4Å: Chain B: R.442 Chain C: T.238, E.262, D.343 Ligands: ADP.5 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:T.238, C:E.262, C:E.262 MG.8: 5 residues within 4Å: Chain C: R.442 Chain D: T.238, E.262, D.343 Ligands: ADP.7 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:T.238, D:E.262, D:E.262 MG.10: 5 residues within 4Å: Chain D: R.442 Chain E: T.238, E.262, D.343 Ligands: ADP.9 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:T.238, E:E.262, E:E.262 MG.12: 5 residues within 4Å: Chain E: R.442 Chain F: T.238, E.262, D.343 Ligands: ADP.11 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:T.238, F:E.262, F:E.262 MG.14: 4 residues within 4Å: Chain G: K.112, N.113, D.169 Ligands: ADP.13 No protein-ligand interaction detected (PLIP) MG.16: 5 residues within 4Å: Chain G: R.220 Chain H: K.112, N.113, D.169 Ligands: 08T.15 No protein-ligand interaction detected (PLIP) MG.18: 5 residues within 4Å: Chain H: R.220 Chain I: K.112, N.113, D.169 Ligands: 08T.17 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:D.169 MG.20: 5 residues within 4Å: Chain I: R.220 Chain J: K.112, N.113, D.169 Ligands: 08T.19 1 PLIP interactions: 1 interactions with chain J Metal complexes: J:D.169 MG.22: 5 residues within 4Å: Chain J: R.220 Chain K: K.112, N.113, D.169 Ligands: 08T.21 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:D.169 MG.24: 5 residues within 4Å: Chain K: R.220 Chain L: K.112, N.113, D.169 Ligands: 08T.23 1 PLIP interactions: 1 interactions with chain L Metal complexes: L:D.169

5 x 08T: [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium(Non-covalent)

08T.15: 20 residues within 4Å: Chain G: R.216, R.220 Chain H: L.65, H.66, N.73, Y.74, R.75, P.108, G.109, T.110, G.111, K.112, N.113, H.114, N.203, W.233, Y.236, R.237, V.240 Ligands: MG.16 13 PLIP interactions: 13 interactions with chain H Hydrogen bonds: H:R.75, H:R.75, H:G.109, H:T.110, H:G.111, H:K.112, H:N.113, H:H.114 Salt bridges: H:H.66, H:K.112, H:R.237, H:R.237 pi-Stacking: H:H.114 08T.17: 20 residues within 4Å: Chain H: R.216, R.220 Chain I: L.65, H.66, N.73, Y.74, R.75, P.108, G.109, T.110, G.111, K.112, N.113, H.114, N.203, W.233, Y.236, R.237, V.240 Ligands: MG.18 17 PLIP interactions: 17 interactions with chain I Hydrogen bonds: I:L.65, I:R.75, I:R.75, I:G.109, I:T.110, I:G.111, I:K.112, I:N.113, I:H.114 Salt bridges: I:H.66, I:K.112, I:R.237, I:R.237 pi-Stacking: I:H.114, I:H.114, I:Y.236, I:Y.236 08T.19: 20 residues within 4Å: Chain I: R.216, R.220 Chain J: L.65, H.66, N.73, Y.74, R.75, P.108, G.109, T.110, G.111, K.112, N.113, H.114, N.203, W.233, Y.236, R.237, V.240 Ligands: MG.20 13 PLIP interactions: 13 interactions with chain J Hydrogen bonds: J:R.75, J:G.109, J:T.110, J:G.111, J:K.112, J:N.113, J:H.114 Salt bridges: J:H.66, J:K.112, J:R.237, J:R.237 pi-Stacking: J:H.114, J:H.114 08T.21: 19 residues within 4Å: Chain J: R.216, R.220 Chain K: L.65, H.66, N.73, Y.74, R.75, P.108, G.109, T.110, G.111, K.112, N.113, H.114, W.233, Y.236, R.237, V.240 Ligands: MG.22 13 PLIP interactions: 12 interactions with chain K, 1 interactions with chain J Hydrogen bonds: K:R.75, K:R.75, K:G.109, K:T.110, K:G.111, K:K.112, K:N.113, K:H.114, J:R.220 Salt bridges: K:H.66, K:K.112, K:R.237 pi-Stacking: K:H.114 08T.23: 20 residues within 4Å: Chain K: R.216, R.220 Chain L: L.65, H.66, N.73, Y.74, R.75, P.108, G.109, T.110, G.111, K.112, N.113, H.114, N.203, W.233, Y.236, R.237, V.240 Ligands: MG.24 12 PLIP interactions: 12 interactions with chain L Hydrogen bonds: L:R.75, L:G.109, L:T.110, L:G.111, L:K.112, L:N.113, L:H.114 Salt bridges: L:H.66, L:K.112, L:R.237, L:R.237 pi-Stacking: L:H.114

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arias-Palomo, E. et al., Physical Basis for the Loading of a Bacterial Replicative Helicase onto DNA. Mol.Cell (2019)

Release Date

2019-03-06

Peptides

Replicative DNA helicase: ABCDEF
DNA replication protein dnaC: GHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

Replicative DNA helicase

DNA replication protein dnaC

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