SMTL ID : 6qem.1

E. coli DnaBC complex bound to ssDNA

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-6-6-mer

Ligands

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.1: 27 residues within 4Å: Chain A: R.232, P.233, S.234, M.235, G.236, K.237, T.238, T.239, E.262, M.263, R.271, Q.281, T.282, Q.384, R.420, F.453, G.455, Q.456 Chain F: Q.410, K.440, Q.441, R.442, N.443, G.444, P.445, I.446 Ligands: MG.2 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:M.235, A:G.236, A:K.237, A:T.238, A:T.239, A:T.239, A:R.420, A:R.420, F:Q.441 Salt bridges: A:K.237, A:R.271 08T.3: 25 residues within 4Å: Chain A: Q.410, K.440, Q.441, R.442, N.443, G.444, P.445, I.446 Chain B: R.232, P.233, S.234, M.235, G.236, K.237, T.238, T.239, E.262, R.271, Q.281, T.282, Q.384, F.453, G.455, Q.456 Ligands: MG.4 9 PLIP interactions: 8 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:M.235, B:G.236, B:K.237, B:T.238, B:T.239, B:T.239, A:Q.441 Salt bridges: B:K.237, B:R.271 08T.5: 24 residues within 4Å: Chain B: Q.410, K.440, Q.441, R.442, N.443, G.444, P.445, I.446 Chain C: R.232, P.233, S.234, M.235, G.236, K.237, T.238, T.239, E.262, R.271, T.282, Q.384, F.453, G.455, Q.456 Ligands: MG.6 11 PLIP interactions: 8 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:M.235, C:G.236, C:K.237, C:T.238, C:T.239, C:T.239, B:Q.441, B:Q.441 Salt bridges: C:K.237, C:R.271, B:K.440 08T.7: 25 residues within 4Å: Chain C: Q.410, K.440, Q.441, R.442, N.443, G.444, P.445, I.446 Chain D: P.233, S.234, M.235, 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 Ligands: MG.8 13 PLIP interactions: 11 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:M.235, D:G.236, D:K.237, D:T.238, D:T.239, D:Q.281, D:Q.384, D:R.420, D:R.420, C:Q.441, C:G.444 Salt bridges: D:K.237, D:R.271 08T.9: 26 residues within 4Å: Chain D: Q.410, K.440, Q.441, R.442, N.443, G.444, P.445, I.446 Chain E: R.232, P.233, S.234, M.235, 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 Ligands: MG.10 10 PLIP interactions: 9 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:G.236, E:K.237, E:T.238, E:T.239, E:T.239, E:Q.281, E:R.420, D:Q.441 Salt bridges: E:K.237, E:R.271

5 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain A: T.238, E.262, M.263, D.343 Ligands: 08T.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.238, A:E.262 MG.4: 5 residues within 4Å: Chain A: R.442 Chain B: T.238, E.262, D.343 Ligands: 08T.3 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.238, B:E.262 MG.6: 6 residues within 4Å: Chain B: R.442 Chain C: T.238, E.262, M.263, D.343 Ligands: 08T.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:T.238 MG.8: 5 residues within 4Å: Chain D: K.237, T.238, E.262, D.343 Ligands: 08T.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:T.238 MG.10: 5 residues within 4Å: Chain D: R.442 Chain E: T.238, E.262, D.343 Ligands: 08T.9 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:T.238, E:E.262

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

ADP.11: 18 residues within 4Å: Chain G: H.66, N.73, Y.74, R.75, Q.81, K.107, P.108, G.109, T.110, G.111, K.112, N.113, H.114, Y.236, R.237 Chain L: R.216, D.219, R.220 22 PLIP interactions: 20 interactions with chain G, 2 interactions with chain L Hydrogen bonds: G:H.66, 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, G:R.237, G:R.237, L:R.220 Salt bridges: G:H.66, G:K.112, G:K.112, L:R.216 pi-Stacking: G:H.114, G:H.114, G:Y.236, G:Y.236 ADP.12: 15 residues within 4Å: Chain G: R.216, D.219 Chain H: H.66, N.73, Y.74, R.75, Q.81, P.108, G.109, T.110, G.111, K.112, N.113, H.114, Y.236 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:N.113, H:H.114 Salt bridges: H:H.66, H:K.112 pi-Stacking: H:H.114, H:H.114 ADP.13: 18 residues within 4Å: Chain H: R.216, D.219, R.220 Chain I: H.66, N.73, Y.74, R.75, Q.81, P.108, G.109, T.110, G.111, K.112, N.113, H.114, W.233, Y.236, R.237 18 PLIP interactions: 2 interactions with chain H, 16 interactions with chain I Hydrogen bonds: H:R.220, I:H.66, I:R.75, I:R.75, I:G.109, I:T.110, I:G.111, I:K.112, I:N.113, I:N.113, I:H.114, I:H.114 Salt bridges: H:R.216, I:K.112, I:K.112 pi-Stacking: I:H.114, I:Y.236, I:Y.236 ADP.14: 17 residues within 4Å: Chain I: R.216, D.219, 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, Y.236, R.237 17 PLIP interactions: 16 interactions with chain J, 1 interactions with chain I Hydrogen bonds: J:R.75, J:R.75, J:G.109, J:T.110, J:G.111, J:K.112, J:N.113, J:N.113, J:H.114, J:R.237, J:R.237 Salt bridges: J:H.66, J:K.112, I:R.216 pi-Stacking: J:H.114, J:Y.236, J:Y.236 ADP.15: 18 residues within 4Å: Chain J: R.216, D.219, R.220 Chain K: H.66, N.73, Y.74, R.75, Q.81, P.108, G.109, T.110, G.111, K.112, N.113, H.114, W.233, Y.236, R.237 17 PLIP interactions: 16 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, K:R.237, K:R.237, J:R.216 Salt bridges: K:H.66, K:K.112 pi-Stacking: K:H.114, K:H.114, K:Y.236, K:Y.236 ADP.16: 16 residues within 4Å: Chain L: L.65, H.66, C.69, N.73, Y.74, R.75, Q.81, P.108, G.109, T.110, G.111, K.112, N.113, H.114, W.233, Y.236 15 PLIP interactions: 15 interactions with chain L Hydrogen bonds: L:H.66, L:R.75, L:G.109, L:T.110, L:T.110, L:G.111, L:K.112, L:N.113, L:H.114, L:H.114 Salt bridges: L:H.66, L:K.112 pi-Stacking: L:H.114, L:Y.236, L:Y.236

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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