SMTL ID : 6jis.1

Crystal structure of the histidine racemase CntK in cobalt and nickel transporter system of staphylococcus aureus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

homo-dimer

Ligands

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

CL.1: 4 residues within 4Å: Chain A: W.188, S.189, Y.192 Ligands: CS.14 Ligand excluded by PLIP CL.2: 2 residues within 4Å: Chain A: D.40, S.42 Ligand excluded by PLIP CL.3: 2 residues within 4Å: Chain A: I.216, Q.217 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain B: W.188, S.189, Y.192 Ligands: CS.28 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain B: D.40, S.42 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain B: I.216, Q.217 Ligand excluded by PLIP

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

EDO.4: 4 residues within 4Å: Chain A: H.95, Q.127, V.276, T.277 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.95 Water bridges: A:V.276 EDO.5: 6 residues within 4Å: Chain A: Q.107, Q.120, E.130, Q.132, S.271 Ligands: EDO.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.107, A:Q.107 EDO.6: 2 residues within 4Å: Chain A: G.114, S.116 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.116, A:S.116 Water bridges: A:G.114, A:T.160 EDO.7: 3 residues within 4Å: Chain A: E.130, S.271 Ligands: EDO.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.130, A:S.271 Water bridges: A:Q.107 EDO.18: 4 residues within 4Å: Chain B: H.95, Q.127, V.276, T.277 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.129, B:Y.129 Water bridges: B:V.276 EDO.19: 6 residues within 4Å: Chain B: Q.107, Q.120, E.130, Q.132, S.271 Ligands: EDO.21 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.107, B:Q.107 EDO.20: 2 residues within 4Å: Chain B: G.114, S.116 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.116, B:S.116 Water bridges: B:G.114, B:T.160 EDO.21: 3 residues within 4Å: Chain B: E.130, S.271 Ligands: EDO.19 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.130, B:S.271 Water bridges: B:Q.107

14 x CS: CESIUM ION(Non-covalent)

CS.8: 2 residues within 4Å: Chain A: D.246, T.248 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.246 CS.9: 2 residues within 4Å: Chain A: K.245, D.246 No protein-ligand interaction detected (PLIP) CS.10: 1 residues within 4Å: Chain A: D.40 No protein-ligand interaction detected (PLIP) CS.11: 4 residues within 4Å: Chain A: V.183, R.184, Q.186, Y.212 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:Q.186, A:Y.212 CS.12: 3 residues within 4Å: Chain A: E.84, Y.161, S.227 No protein-ligand interaction detected (PLIP) CS.13: 3 residues within 4Å: Chain A: M.52, C.58, C.59 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:M.52 CS.14: 4 residues within 4Å: Chain A: Q.186, Q.187, W.188 Ligands: CL.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:Q.187 CS.22: 2 residues within 4Å: Chain B: D.246, T.248 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.246 CS.23: 2 residues within 4Å: Chain B: K.245, D.246 No protein-ligand interaction detected (PLIP) CS.24: 1 residues within 4Å: Chain B: D.40 No protein-ligand interaction detected (PLIP) CS.25: 4 residues within 4Å: Chain B: V.183, R.184, Q.186, Y.212 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:Q.186, B:Y.212 CS.26: 3 residues within 4Å: Chain B: E.84, Y.161, S.227 No protein-ligand interaction detected (PLIP) CS.27: 3 residues within 4Å: Chain B: M.52, C.58, C.59 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:M.52 CS.28: 4 residues within 4Å: Chain B: Q.186, Q.187, W.188 Ligands: CL.15 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:Q.187

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Luo, S. et al., Crystal structure of CntK, the cofactor-independent histidine racemase in staphylopine-mediated metal acquisition of Staphylococcus aureus. Int.J.Biol.Macromol. (2019)

Release Date

2019-10-16

Peptides

Diaminopimelate epimerase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Diaminopimelate epimerase