SMTL ID : 4pu9.1

E. coli GyrB 43-kDa N-terminal fragment in complex with ADP-BeF3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 23 residues within 4Å: Chain A: N.52, E.56, D.79, I.84, I.100, A.106, G.107, G.108, K.109, Y.115, G.120, L.121, H.122, G.123, V.124, G.125, V.126, S.127, T.171 Chain B: Y.11, I.16 Ligands: BEF.2, MG.3 18 PLIP interactions: 17 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.52, A:E.56, A:D.79, A:G.108, A:K.109, A:L.121, A:H.122, A:G.123, A:V.124, A:V.124, A:G.125, A:V.126, A:S.127, B:Y.11 Water bridges: A:T.171, A:T.171 Salt bridges: A:K.109 pi-Cation interactions: A:K.109 ADP.4: 23 residues within 4Å: Chain A: Y.11, I.16 Chain B: N.52, E.56, D.79, I.84, I.100, A.106, G.107, G.108, K.109, Y.115, G.120, L.121, H.122, G.123, V.124, G.125, V.126, S.127, T.171 Ligands: BEF.5, MG.6 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.79, B:G.108, B:K.109, B:Y.115, B:L.121, B:H.122, B:G.123, B:V.124, B:V.124, B:G.125, B:V.126, B:S.127, B:T.171, A:Y.11 Salt bridges: B:K.109 pi-Cation interactions: B:K.109

2 x BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)

BEF.2: 9 residues within 4Å: Chain A: G.120, L.121, H.122, G.123, V.124, G.125, K.343 Ligands: ADP.1, MG.3 No protein-ligand interaction detected (PLIP) BEF.5: 9 residues within 4Å: Chain B: G.120, L.121, H.122, G.123, V.124, G.125, K.343 Ligands: ADP.4, MG.6 No protein-ligand interaction detected (PLIP)

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: N.52, K.109 Ligands: ADP.1, BEF.2 No protein-ligand interaction detected (PLIP) MG.6: 4 residues within 4Å: Chain B: N.52, K.109 Ligands: ADP.4, BEF.5 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Stanger, F.V. et al., Structure of the N-Terminal Gyrase B Fragment in Complex with ADPPi Reveals Rigid-Body Motion Induced by ATP Hydrolysis. Plos One (2014)

Release Date

2014-09-24

Peptides

GyrB: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

GyrB

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