SMTL ID : 3zkd.3 (3 other biounits)

CRYSTAL STRUCTURE OF THE ATPASE REGION OF Mycobacterium tuberculosis GyrB WITH AMPPNP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.95 Å

Oligo State

homo-dimer

Ligands

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

ANP.1: 27 residues within 4Å: Chain A: E.53, N.57, A.58, E.61, D.84, G.88, I.89, V.104, A.110, G.111, G.112, K.113, Y.119, G.124, L.125, H.126, G.127, V.128, G.129, V.130, S.131, S.174, Q.375, K.377 Chain B: Y.17, I.22 Ligands: MG.2 25 PLIP interactions: 24 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.57, A:E.61, A:D.84, A:G.112, A:K.113, A:K.113, A:K.113, A:Y.119, A:L.125, A:H.126, A:H.126, A:G.127, A:V.128, A:G.129, A:V.130, A:S.131, A:S.174, A:Q.375, A:Q.375, A:K.377, B:Y.17 Water bridges: A:G.88, A:G.111 Salt bridges: A:K.113 pi-Cation interactions: A:K.113 ANP.3: 27 residues within 4Å: Chain A: Y.17, I.22 Chain B: E.53, N.57, A.58, E.61, D.84, G.88, I.89, V.104, A.110, G.111, G.112, K.113, Y.119, G.124, L.125, H.126, G.127, V.128, G.129, V.130, S.131, S.174, Q.375, K.377 Ligands: MG.4 22 PLIP interactions: 21 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.57, B:D.84, B:G.112, B:K.113, B:K.113, B:K.113, B:Y.119, B:L.125, B:H.126, B:G.127, B:V.128, B:G.129, B:V.130, B:S.131, B:S.174, B:Q.375, B:K.377, A:Y.17 Water bridges: B:G.88, B:G.111, B:G.111 pi-Cation interactions: B:K.113

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: E.53, N.57, G.129 Ligands: ANP.1 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain B: E.53, N.57 Ligands: ANP.3 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Agrawal, A. et al., Mycobacterium Tuberculosis DNA Gyrase ATPase Domain Structures Suggest a Dissociative Mechanism that Explains How ATP Hydrolysis is Coupled to Domain Motion. Biochem.J. (2013)

Release Date

2013-09-18

Peptides

DNA GYRASE SUBUNIT B: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

DNA GYRASE SUBUNIT B

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