SMTL ID : 3af0.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x GDP: GUANOSINE-5'-DIPHOSPHATE(Non-covalent)

GDP.1: 14 residues within 4Å: Chain A: S.98, V.99, A.100, V.101, G.102, K.103, S.104, H.179, L.180, R.238, M.242, A.246, F.247 Ligands: PAU.2 17 PLIP interactions: 17 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:R.238 Water bridges: A:L.40, A:G.102, A:T.105, A:H.179, A:R.238 Salt bridges: A:K.103, A:K.103, A:R.238 pi-Stacking: A:H.179 GDP.13: 14 residues within 4Å: Chain B: S.98, V.99, A.100, V.101, G.102, K.103, S.104, H.179, L.180, R.238, M.242, A.246, F.247 Ligands: PAU.14 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:G.102, B:T.105, B:H.179, B:Y.235, B:R.238 Salt bridges: B:K.103, B:K.103, B:R.238 pi-Stacking: B:H.179

2 x PAU: PANTOTHENOIC ACID(Non-covalent)

PAU.2: 9 residues within 4Å: Chain A: V.99, D.129, L.132, K.147, G.148, Y.153, H.179, Y.182 Ligands: GDP.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.147, A:Y.182 PAU.14: 9 residues within 4Å: Chain B: V.99, D.129, L.132, K.147, G.148, Y.153, H.179, Y.182 Ligands: GDP.13 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.147 Water bridges: B:Y.235

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

CL.3: 4 residues within 4Å: Chain A: T.128, L.203, N.204, V.205 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain B: T.128, L.203, N.204, V.205 Ligand excluded by PLIP

18 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: Y.177, S.178, H.179, L.180 Ligand excluded by PLIP GOL.5: 7 residues within 4Å: Chain B: F.218, D.219, F.220, S.221, R.291, T.293, R.310 Ligand excluded by PLIP GOL.6: 3 residues within 4Å: Chain A: F.161, A.172, C.173 Ligand excluded by PLIP GOL.7: 6 residues within 4Å: Chain A: Q.207, T.208, P.287, R.291 Chain B: G.209, P.210 Ligand excluded by PLIP GOL.8: 6 residues within 4Å: Chain A: D.225, A.226, R.227, R.289, R.297, R.306 Ligand excluded by PLIP GOL.9: 4 residues within 4Å: Chain A: A.115, R.122, V.123, D.124 Ligand excluded by PLIP GOL.10: 3 residues within 4Å: Chain A: G.36, R.38, R.108 Ligand excluded by PLIP GOL.11: 2 residues within 4Å: Chain A: A.188, E.189 Ligand excluded by PLIP GOL.12: 3 residues within 4Å: Chain A: R.122, R.193, H.194 Ligand excluded by PLIP GOL.16: 4 residues within 4Å: Chain B: Y.177, S.178, H.179, L.180 Ligand excluded by PLIP GOL.17: 7 residues within 4Å: Chain A: F.218, D.219, F.220, S.221, R.291, T.293, R.310 Ligand excluded by PLIP GOL.18: 3 residues within 4Å: Chain B: F.161, A.172, C.173 Ligand excluded by PLIP GOL.19: 6 residues within 4Å: Chain A: G.209, P.210 Chain B: Q.207, T.208, P.287, R.291 Ligand excluded by PLIP GOL.20: 6 residues within 4Å: Chain B: D.225, A.226, R.227, R.289, R.297, R.306 Ligand excluded by PLIP GOL.21: 4 residues within 4Å: Chain B: A.115, R.122, V.123, D.124 Ligand excluded by PLIP GOL.22: 3 residues within 4Å: Chain B: G.36, R.38, R.108 Ligand excluded by PLIP GOL.23: 2 residues within 4Å: Chain B: A.188, E.189 Ligand excluded by PLIP GOL.24: 3 residues within 4Å: Chain B: R.122, R.193, H.194 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chetnani, B. et al., M. tuberculosis pantothenate kinase: dual substrate specificity and unusual changes in ligand locations. J.Mol.Biol. (2010)

Release Date

2010-05-26

Peptides

Pantothenate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Pantothenate kinase

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