SMTL ID : 4ijn.1

Crystal structure of an acetate kinase from Mycobacterium smegmatis bound to AMP and sulfate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 8 residues within 4Å: Chain A: R.93, H.125, H.182, N.213, G.214, R.243 Ligands: AMP.2, EDO.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.214 Water bridges: A:H.125, A:N.213 Salt bridges: A:R.93, A:H.125, A:H.182, A:R.243 SO4.5: 8 residues within 4Å: Chain B: R.93, H.125, H.182, N.213, G.214, R.243 Ligands: AMP.6, EDO.7 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.214 Water bridges: B:R.93, B:H.182, B:N.213 Salt bridges: B:R.93, B:H.125, B:H.182, B:R.243

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.2: 11 residues within 4Å: Chain A: G.212, N.213, D.284, F.285, R.286, A.331, G.332, V.333, N.336, V.337 Ligands: SO4.1 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:N.213, A:N.213, A:D.284, A:F.285, A:R.286, A:G.332, A:N.336 Water bridges: A:K.36, A:N.213, A:G.214, A:R.286, A:R.286 Salt bridges: A:K.36 pi-Cation interactions: A:R.286 AMP.6: 11 residues within 4Å: Chain B: G.212, N.213, D.284, F.285, R.286, A.331, G.332, V.333, N.336, V.337 Ligands: SO4.5 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:N.213, B:N.213, B:D.284, B:F.285, B:R.286, B:R.286, B:G.332, B:N.336 Water bridges: B:H.210, B:N.213, B:N.213

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 7 residues within 4Å: Chain A: E.202, S.203, L.204, N.205, A.221, G.222, R.323 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.323, A:R.323 EDO.4: 10 residues within 4Å: Chain A: R.93, V.95, H.125, D.150, F.181, H.182, M.230, P.234, R.243 Ligands: SO4.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.93, A:D.150, A:H.182, A:H.182, A:R.243, A:R.243 EDO.7: 11 residues within 4Å: Chain B: R.93, V.95, H.125, D.150, F.181, H.182, G.214, M.230, P.234, R.243 Ligands: SO4.5 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.182, B:R.243, B:R.243

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baugh, L. et al., Increasing the structural coverage of tuberculosis drug targets. Tuberculosis (Edinb) (2015)

Release Date

2013-01-16

Peptides

Acetate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Acetate kinase