SMTL ID : 3aez.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 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, R.238, M.242, A.246, F.247 Ligands: PAZ.2, GOL.15 20 PLIP interactions: 20 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:G.102, A:K.103, A:K.103, A:R.108, A:R.108, A:H.179, A:R.238, A:R.238 Salt bridges: A:K.103, A:K.103, A:R.238 pi-Stacking: A:H.179 GDP.17: 14 residues within 4Å: Chain B: S.98, V.99, A.100, V.101, G.102, K.103, S.104, H.179, R.238, M.242, A.246, F.247 Ligands: PAZ.18, GOL.31 21 PLIP interactions: 21 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:E.201, B:R.238 Water bridges: B:G.102, B:K.103, B:K.103, B:R.108, B:R.108, B:H.179, B:R.238, B:R.238 Salt bridges: B:K.103, B:K.103, B:R.238 pi-Stacking: B:H.179

2 x PAZ: N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanine(Non-covalent)

PAZ.2: 13 residues within 4Å: Chain A: V.99, T.128, D.129, G.148, Y.153, H.179, Y.182, E.201, G.202, L.203, I.276 Ligands: GDP.1, GOL.8 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:D.129 Hydrogen bonds: A:T.128, A:T.128, A:T.128, A:D.129, A:Y.182, A:L.203 Water bridges: A:K.147, A:Y.182, A:N.204 PAZ.18: 13 residues within 4Å: Chain B: V.99, T.128, D.129, G.148, Y.153, H.179, Y.182, E.201, G.202, L.203, I.276 Ligands: GDP.17, GOL.24 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:D.129 Hydrogen bonds: B:T.128, B:T.128, B:D.129, B:Y.153, B:L.203 Water bridges: B:K.147, B:Y.182, B:N.204, B:Y.235

26 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: R.146, F.149, E.283 Ligands: GOL.9 Ligand excluded by PLIP GOL.4: 7 residues within 4Å: Chain A: G.209, P.210 Chain B: Q.207, T.208, P.287, T.288, R.291 Ligand excluded by PLIP GOL.5: 5 residues within 4Å: Chain A: R.291, R.310 Chain B: D.216 Ligands: GOL.6, GOL.21 Ligand excluded by PLIP GOL.6: 8 residues within 4Å: Chain A: F.218, D.219, F.220, S.221, R.291, T.293, R.310 Ligands: GOL.5 Ligand excluded by PLIP GOL.7: 6 residues within 4Å: Chain A: D.225, A.226, R.227, R.289, R.297, R.306 Ligand excluded by PLIP GOL.8: 6 residues within 4Å: Chain A: H.145, Y.182, F.254, I.272, I.276 Ligands: PAZ.2 Ligand excluded by PLIP GOL.9: 6 residues within 4Å: Chain A: R.146, F.149, E.151, E.283, N.284 Ligands: GOL.3 Ligand excluded by PLIP GOL.10: 2 residues within 4Å: Chain A: P.175, G.187 Ligand excluded by PLIP GOL.11: 6 residues within 4Å: Chain A: R.15, Q.43, I.44, E.48, D.301, S.303 Ligand excluded by PLIP GOL.12: 5 residues within 4Å: Chain A: S.178, H.179, L.180, H.181 Ligands: GOL.14 Ligand excluded by PLIP GOL.13: 8 residues within 4Å: Chain A: P.150, R.155, L.158, N.204, V.205, Q.207, M.213, V.214 Ligand excluded by PLIP GOL.14: 5 residues within 4Å: Chain A: D.129, Y.177, S.178, H.179 Ligands: GOL.12 Ligand excluded by PLIP GOL.15: 6 residues within 4Å: Chain A: Y.235, R.238, F.239, M.242, F.247 Ligands: GDP.1 Ligand excluded by PLIP GOL.19: 4 residues within 4Å: Chain B: R.146, F.149, E.283 Ligands: GOL.25 Ligand excluded by PLIP GOL.20: 7 residues within 4Å: Chain A: Q.207, T.208, P.287, T.288, R.291 Chain B: G.209, P.210 Ligand excluded by PLIP GOL.21: 5 residues within 4Å: Chain A: D.216 Chain B: R.291, R.310 Ligands: GOL.5, GOL.22 Ligand excluded by PLIP GOL.22: 8 residues within 4Å: Chain B: F.218, D.219, F.220, S.221, R.291, T.293, R.310 Ligands: GOL.21 Ligand excluded by PLIP GOL.23: 6 residues within 4Å: Chain B: D.225, A.226, R.227, R.289, R.297, R.306 Ligand excluded by PLIP GOL.24: 6 residues within 4Å: Chain B: H.145, Y.182, F.254, I.272, I.276 Ligands: PAZ.18 Ligand excluded by PLIP GOL.25: 6 residues within 4Å: Chain B: R.146, F.149, E.151, E.283, N.284 Ligands: GOL.19 Ligand excluded by PLIP GOL.26: 2 residues within 4Å: Chain B: P.175, G.187 Ligand excluded by PLIP GOL.27: 6 residues within 4Å: Chain B: R.15, Q.43, I.44, E.48, D.301, S.303 Ligand excluded by PLIP GOL.28: 5 residues within 4Å: Chain B: S.178, H.179, L.180, H.181 Ligands: GOL.30 Ligand excluded by PLIP GOL.29: 8 residues within 4Å: Chain B: P.150, R.155, L.158, N.204, V.205, Q.207, M.213, V.214 Ligand excluded by PLIP GOL.30: 5 residues within 4Å: Chain B: D.129, Y.177, S.178, H.179 Ligands: GOL.28 Ligand excluded by PLIP GOL.31: 6 residues within 4Å: Chain B: Y.235, R.238, F.239, M.242, F.247 Ligands: GDP.17 Ligand excluded by PLIP

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

NA.16: 5 residues within 4Å: Chain A: E.42, A.100, V.101, G.102, H.302 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.42, A:E.42 Water bridges: A:R.238 NA.32: 5 residues within 4Å: Chain B: E.42, A.100, V.101, G.102, H.302 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.100 Water bridges: B:R.238

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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