SMTL ID : 4prx.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 27 residues within 4Å: Chain A: N.52, A.53, E.56, D.79, R.82, G.83, I.84, P.85, 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: PO4.2, MG.3 21 PLIP interactions: 20 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.52, A:D.79, A:G.108, A:K.109, A:K.109, A:Y.115, A:L.121, A:H.122, A:G.123, A:V.124, A:G.125, A:V.126, A:S.127, A:T.171, B:Y.11 Water bridges: A:A.53, A:A.53, A:D.79, A:S.127 Salt bridges: A:K.109 pi-Cation interactions: A:K.109 ADP.5: 27 residues within 4Å: Chain A: Y.11, I.16 Chain B: N.52, A.53, E.56, D.79, R.82, G.83, I.84, P.85, 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: PO4.6, MG.7 22 PLIP interactions: 1 interactions with chain A, 21 interactions with chain B Hydrogen bonds: A:Y.11, B:N.52, B:E.56, B:D.79, B:G.108, B:K.109, B:K.109, B:Y.115, B:L.121, B:H.122, B:G.123, B:V.124, B:G.125, B:V.126, B:S.127, B:T.171 Water bridges: B:A.53, B:D.79, B:D.79, B:S.127 Salt bridges: B:K.109 pi-Cation interactions: B:K.109

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 11 residues within 4Å: Chain A: E.48, G.120, L.121, H.122, G.123, V.124, G.125, Q.341, K.343 Ligands: ADP.1, MG.3 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:L.121, A:H.122, A:G.123, A:V.124, A:G.125 Water bridges: A:E.48, A:E.48, A:N.52, A:G.119, A:K.343, A:K.343 Salt bridges: A:H.122, A:K.343 PO4.6: 11 residues within 4Å: Chain B: E.48, G.120, L.121, H.122, G.123, V.124, G.125, Q.341, K.343 Ligands: ADP.5, MG.7 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:L.121, B:H.122, B:G.123, B:V.124, B:G.125 Water bridges: B:E.48, B:E.48, B:N.52, B:G.119, B:K.343, B:K.343 Salt bridges: B:H.122, B:K.343

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 7 residues within 4Å: Chain A: E.48, N.52, K.109, G.120, G.125 Ligands: ADP.1, PO4.2 No protein-ligand interaction detected (PLIP) MG.7: 7 residues within 4Å: Chain B: E.48, N.52, K.109, G.120, G.125 Ligands: ADP.5, PO4.6 No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: D.72, Q.134, W.176 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.72, A:Q.134 GOL.8: 3 residues within 4Å: Chain B: D.72, Q.134, W.176 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Q.134

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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