SMTL ID : 3r20.2 (2 other biounits)

Crystal structure of cytidylate kinase from Mycobacterium smegmatis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-trimer

Ligands

3 x DPO: DIPHOSPHATE(Non-covalent)

DPO.1: 11 residues within 4Å: Chain A: P.17, A.18, G.19, T.20, G.21, K.22, S.23, S.24, E.134, R.162, Q.166 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:P.17, A:G.19, A:T.20, A:G.21, A:G.21, A:K.22, A:S.23, A:S.24, A:E.134, A:Q.166, A:Q.166 Water bridges: A:K.22, A:S.23, A:S.23, A:R.162 Salt bridges: A:K.22, A:R.162 DPO.5: 11 residues within 4Å: Chain B: P.17, A.18, G.19, T.20, G.21, K.22, S.23, S.24, E.134, R.162, Q.166 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:P.17, B:G.19, B:T.20, B:G.21, B:G.21, B:K.22, B:S.23, B:S.24, B:E.134, B:Q.166, B:Q.166 Water bridges: B:K.22, B:S.23, B:S.23, B:R.162 Salt bridges: B:K.22, B:R.162 DPO.9: 11 residues within 4Å: Chain C: P.17, A.18, G.19, T.20, G.21, K.22, S.23, S.24, E.134, R.162, Q.166 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:P.17, C:G.19, C:T.20, C:G.21, C:G.21, C:K.22, C:S.23, C:S.24, C:E.134, C:Q.166, C:Q.166 Water bridges: C:K.22, C:S.23, C:S.23, C:R.162 Salt bridges: C:K.22, C:R.162

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

EDO.2: 7 residues within 4Å: Chain A: R.27, D.39, A.42, V.81, D.82, A.83, R.96 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.27, A:R.27, A:D.39, A:A.83, A:R.96 Water bridges: A:G.76, A:V.81, A:D.82, A:D.82 EDO.6: 7 residues within 4Å: Chain B: R.27, D.39, A.42, V.81, D.82, A.83, R.96 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:R.27, B:R.27, B:D.39, B:A.83, B:R.96 Water bridges: B:G.76, B:V.81, B:D.82, B:D.82 EDO.10: 7 residues within 4Å: Chain C: R.27, D.39, A.42, V.81, D.82, A.83, R.96 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:R.27, C:R.27, C:D.39, C:A.83, C:R.96 Water bridges: C:G.76, C:V.81, C:D.82, C:D.82

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 1 residues within 4Å: Chain A: R.45 Ligand excluded by PLIP CL.7: 1 residues within 4Å: Chain B: R.45 Ligand excluded by PLIP CL.11: 1 residues within 4Å: Chain C: R.45 Ligand excluded by PLIP

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

SO4.4: 2 residues within 4Å: Chain A: R.185, H.188 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.185, A:R.185 Salt bridges: A:R.185, A:H.188 SO4.8: 2 residues within 4Å: Chain B: R.185, H.188 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.185, B:R.185 Salt bridges: B:R.185, B:H.188 SO4.12: 2 residues within 4Å: Chain C: R.185, H.188 4 PLIP interactions: 4 interactions with chain C Water bridges: C:R.185, C:R.185 Salt bridges: C:R.185, C:H.188

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

2011-04-13

Peptides

Cytidylate kinase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Cytidylate kinase

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