SMTL ID : 6rkw.1

CryoEM structure of the complete E. coli DNA Gyrase complex bound to a 130 bp DNA duplex

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 21 residues within 4Å: Chain C: E.42, N.46, A.47, E.50, I.78, I.94, A.100, G.101, G.102, K.103, Y.109, G.114, L.115, H.116, G.117, V.118, G.119, V.120, Q.335, K.337 Chain D: I.10 19 PLIP interactions: 19 interactions with chain C Hydrogen bonds: C:E.42, C:E.42, C:E.42, C:N.46, C:G.102, C:K.103, C:K.103, C:Y.109, C:L.115, C:H.116, C:H.116, C:H.116, C:G.117, C:V.118, C:G.119, C:V.120, C:K.337 Salt bridges: C:K.103 pi-Cation interactions: C:K.103 ANP.2: 24 residues within 4Å: Chain C: Y.5 Chain D: E.42, N.46, A.47, D.49, E.50, D.73, G.77, I.78, I.94, A.100, G.101, G.102, K.103, Y.109, G.114, L.115, H.116, G.117, V.118, G.119, V.120, T.165, K.337 17 PLIP interactions: 1 interactions with chain C, 16 interactions with chain D Hydrogen bonds: C:Y.5, D:N.46, D:N.46, D:D.49, D:D.73, D:G.102, D:K.103, D:G.114, D:L.115, D:H.116, D:G.117, D:V.118, D:G.119, D:V.120, D:K.337, D:K.337 Salt bridges: D:K.103

1 x JHN: (3~{R})-3-[[4-(3,4-dihydro-2~{H}-pyrano[2,3-c]pyridin-6-ylmethylamino)piperidin-1-yl]methyl]-1,4,7-triazatricyclo[6.3.1.0^{4,12}]dodeca-6,8(12),9-triene-5,11-dione(Non-covalent)

JHN.3: 10 residues within 4Å: Chain A: D.82, M.120 Chain B: A.67, G.71, D.82, M.120 Chain G: T.2, A.3 Chain H: T.2, A.3 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.67 Hydrogen bonds: B:D.82

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vanden Broeck, A. et al., Cryo-EM structure of the complete E. coli DNA gyrase nucleoprotein complex. Nat Commun (2019)

Release Date

2019-11-06

Peptides

DNA gyrase subunit A: AB
DNA gyrase subunit B: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
B

D
D

DNA gyrase subunit A

DNA gyrase subunit B

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