SMTL ID : 3af1.1

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

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: 13 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 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:R.108, A:H.179, A:R.238 Salt bridges: A:K.103, A:K.103, A:R.238 pi-Stacking: A:H.179 GDP.19: 13 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 17 PLIP interactions: 17 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:R.108, B:H.179, B:R.238 Salt bridges: B:K.103, B:K.103, B:R.238 pi-Stacking: B:H.179

2 x FLC: CITRATE ANION(Non-covalent)

FLC.2: 5 residues within 4Å: Chain A: D.129, Y.177, S.178, H.179, L.180 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.129, A:D.129, A:L.180 Water bridges: A:T.127, A:Y.177 Salt bridges: A:H.179 FLC.20: 5 residues within 4Å: Chain B: D.129, Y.177, S.178, H.179, L.180 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.129, B:L.180 Water bridges: B:Y.177, B:Y.177 Salt bridges: B:H.179

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

CL.3: 3 residues within 4Å: Chain A: E.232, Q.233, R.270 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Chain A: T.128, Y.153, N.204, V.205 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: R.155, N.204, Q.207 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain B: E.232, Q.233, R.270 Ligand excluded by PLIP CL.22: 4 residues within 4Å: Chain B: T.128, Y.153, N.204, V.205 Ligand excluded by PLIP CL.23: 3 residues within 4Å: Chain B: R.155, N.204, Q.207 Ligand excluded by PLIP

26 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 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.7: 7 residues within 4Å: Chain A: R.15, Q.43, I.44, D.45, E.48, D.301, S.303 Ligand excluded by PLIP GOL.8: 2 residues within 4Å: Chain A: P.175, E.189 Ligand excluded by PLIP GOL.9: 4 residues within 4Å: Chain A: D.225, A.226, R.289, R.297 Ligand excluded by PLIP GOL.10: 8 residues within 4Å: Chain B: R.67, F.218, F.220, S.221, R.291, T.293, R.310 Ligands: GOL.18 Ligand excluded by PLIP GOL.11: 6 residues within 4Å: Chain A: D.216 Chain B: S.215, R.291, R.310 Ligands: GOL.18, GOL.29 Ligand excluded by PLIP GOL.12: 4 residues within 4Å: Chain A: A.157, R.160, F.161, C.173 Ligand excluded by PLIP GOL.13: 2 residues within 4Å: Chain A: R.122, H.194 Ligand excluded by PLIP GOL.14: 4 residues within 4Å: Chain A: G.41, S.237, R.238, A.241 Ligand excluded by PLIP GOL.15: 4 residues within 4Å: Chain A: Q.111, A.115, R.122, V.123 Ligand excluded by PLIP GOL.16: 5 residues within 4Å: Chain A: R.146, F.149, E.151, E.283, N.284 Ligand excluded by PLIP GOL.17: 3 residues within 4Å: Chain A: G.36, R.38, R.108 Ligand excluded by PLIP GOL.18: 8 residues within 4Å: Chain A: R.67, K.166, D.216, F.218, D.219 Chain B: L.312 Ligands: GOL.10, GOL.11 Ligand excluded by PLIP GOL.24: 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.25: 7 residues within 4Å: Chain B: R.15, Q.43, I.44, D.45, E.48, D.301, S.303 Ligand excluded by PLIP GOL.26: 2 residues within 4Å: Chain B: P.175, E.189 Ligand excluded by PLIP GOL.27: 4 residues within 4Å: Chain B: D.225, A.226, R.289, R.297 Ligand excluded by PLIP GOL.28: 8 residues within 4Å: Chain A: R.67, F.218, F.220, S.221, R.291, T.293, R.310 Ligands: GOL.36 Ligand excluded by PLIP GOL.29: 6 residues within 4Å: Chain A: S.215, R.291, R.310 Chain B: D.216 Ligands: GOL.11, GOL.36 Ligand excluded by PLIP GOL.30: 4 residues within 4Å: Chain B: A.157, R.160, F.161, C.173 Ligand excluded by PLIP GOL.31: 2 residues within 4Å: Chain B: R.122, H.194 Ligand excluded by PLIP GOL.32: 4 residues within 4Å: Chain B: G.41, S.237, R.238, A.241 Ligand excluded by PLIP GOL.33: 4 residues within 4Å: Chain B: Q.111, A.115, R.122, V.123 Ligand excluded by PLIP GOL.34: 5 residues within 4Å: Chain B: R.146, F.149, E.151, E.283, N.284 Ligand excluded by PLIP GOL.35: 3 residues within 4Å: Chain B: G.36, R.38, R.108 Ligand excluded by PLIP GOL.36: 8 residues within 4Å: Chain A: L.312 Chain B: R.67, K.166, D.216, F.218, D.219 Ligands: GOL.28, GOL.29 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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