SMTL ID : 2zs9.1

Pantothenate kinase from Mycobacterium tuberculosis (MtPanK) in complex with ADP and Pantothenate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 15 residues within 4Å: Chain A: S.98, V.99, A.100, V.101, G.102, K.103, S.104, H.179, E.201, R.238, M.242, A.246, F.247 Ligands: GOL.9, PAU.13 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:A.100, A:V.101, A:G.102, A:K.103, A:S.104, A:S.104, A:S.104, A:H.179, A:R.238 Water bridges: A:L.40, A:T.105, A:R.108, A:H.179, A:R.238, A:S.252 Salt bridges: A:K.103, A:K.103, A:R.238 pi-Cation interactions: A:H.179 ADP.14: 15 residues within 4Å: Chain B: S.98, V.99, A.100, V.101, G.102, K.103, S.104, H.179, E.201, R.238, M.242, A.246, F.247 Ligands: GOL.22, PAU.26 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:A.100, B:V.101, B:G.102, B:K.103, B:S.104, B:S.104, B:S.104, B:R.238 Water bridges: B:L.40, B:T.105, B:R.108, B:H.179, B:R.238, B:S.252 Salt bridges: B:K.103, B:K.103, B:R.238 pi-Cation interactions: B:H.179

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: Y.177, S.178, H.179, L.180, I.185 Ligand excluded by PLIP GOL.3: 8 residues within 4Å: Chain A: R.67, F.218, D.219, F.220, S.221, R.291, T.293 Ligands: NA.12 Ligand excluded by PLIP GOL.4: 3 residues within 4Å: Chain A: A.248, H.255, A.258 Ligand excluded by PLIP GOL.5: 3 residues within 4Å: Chain A: R.122, R.193, H.194 Ligand excluded by PLIP GOL.6: 7 residues within 4Å: Chain A: T.208, P.287, T.288, R.291 Chain B: G.209, P.210 Ligands: GOL.19 Ligand excluded by PLIP GOL.7: 5 residues within 4Å: Chain A: R.160, F.161, S.164, A.172, C.173 Ligand excluded by PLIP GOL.8: 4 residues within 4Å: Chain A: L.240, A.241, R.243, T.244 Ligand excluded by PLIP GOL.9: 6 residues within 4Å: Chain A: Y.235, R.238, F.239, F.254 Ligands: ADP.1, PAU.13 Ligand excluded by PLIP GOL.15: 5 residues within 4Å: Chain B: Y.177, S.178, H.179, L.180, I.185 Ligand excluded by PLIP GOL.16: 8 residues within 4Å: Chain B: R.67, F.218, D.219, F.220, S.221, R.291, T.293 Ligands: NA.25 Ligand excluded by PLIP GOL.17: 3 residues within 4Å: Chain B: A.248, H.255, A.258 Ligand excluded by PLIP GOL.18: 3 residues within 4Å: Chain B: R.122, R.193, H.194 Ligand excluded by PLIP GOL.19: 7 residues within 4Å: Chain A: G.209, P.210 Chain B: T.208, P.287, T.288, R.291 Ligands: GOL.6 Ligand excluded by PLIP GOL.20: 5 residues within 4Å: Chain B: R.160, F.161, S.164, A.172, C.173 Ligand excluded by PLIP GOL.21: 4 residues within 4Å: Chain B: L.240, A.241, R.243, T.244 Ligand excluded by PLIP GOL.22: 6 residues within 4Å: Chain B: Y.235, R.238, F.239, F.254 Ligands: ADP.14, PAU.26 Ligand excluded by PLIP

6 x NA: SODIUM ION(Non-functional Binders)

NA.10: 2 residues within 4Å: Chain A: E.48, S.303 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.48 NA.11: 4 residues within 4Å: Chain A: T.127, G.130, P.175, Q.190 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.127, A:T.127, A:G.130 Water bridges: A:T.127 NA.12: 4 residues within 4Å: Chain A: L.206, S.215, F.218 Ligands: GOL.3 2 PLIP interactions: 2 interactions with chain A Water bridges: A:S.215, A:F.218 NA.23: 2 residues within 4Å: Chain B: E.48, S.303 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.48 NA.24: 4 residues within 4Å: Chain B: T.127, G.130, P.175, Q.190 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.127, B:G.130 Water bridges: B:T.127 NA.25: 4 residues within 4Å: Chain B: L.206, S.215, F.218 Ligands: GOL.16 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.215 Water bridges: B:F.218

2 x PAU: PANTOTHENOIC ACID(Non-covalent)

PAU.13: 8 residues within 4Å: Chain A: V.99, D.129, K.147, H.179, Y.182, N.277 Ligands: ADP.1, GOL.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.238, A:N.277 PAU.26: 8 residues within 4Å: Chain B: V.99, D.129, K.147, H.179, Y.182, N.277 Ligands: ADP.14, GOL.22 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.182, B:R.238, B:N.277

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chetnani, B. et al., Mycobacterium tuberculosis pantothenate kinase: possible changes in location of ligands during enzyme action. Acta Crystallogr.,Sect.D (2009)

Release Date

2009-07-21

Peptides

Pantothenate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Pantothenate kinase

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