SMTL ID : 2zsf.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-dimer

Ligands

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 16 residues within 4Å: Chain A: G.39, E.42, V.99, A.100, V.101, G.102, K.103, S.104, T.105, R.108, H.179, R.238, M.242, A.246 Ligands: ADP.2, FLC.9 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:A.100, A:G.102, A:S.104, A:S.104, A:T.105, A:R.108, A:H.179, A:R.238 Water bridges: A:L.40, A:S.104, A:H.179 Salt bridges: A:K.103, A:K.103, A:R.108, A:R.238, A:R.238 pi-Stacking: A:H.179, A:H.179 ATP.14: 16 residues within 4Å: Chain B: G.39, E.42, V.99, A.100, V.101, G.102, K.103, S.104, T.105, R.108, H.179, R.238, M.242, A.246 Ligands: ADP.15, FLC.22 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:A.100, B:G.102, B:S.104, B:S.104, B:T.105, B:T.105, B:R.108, B:H.179, B:H.179, B:R.238 Water bridges: B:L.40, B:S.104, B:H.179 Salt bridges: B:K.103, B:K.103, B:R.108, B:R.238, B:R.238 pi-Stacking: B:H.179, B:H.179

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

ADP.2: 14 residues within 4Å: Chain A: V.99, A.100, V.101, G.102, K.103, S.104, R.108, H.179, R.238, M.242, A.246 Ligands: ATP.1, GOL.8, FLC.9 11 PLIP interactions: 11 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:R.108, A:R.238 Salt bridges: A:K.103, A:K.103, A:R.238 ADP.15: 14 residues within 4Å: Chain B: V.99, A.100, V.101, G.102, K.103, S.104, R.108, H.179, R.238, M.242, A.246 Ligands: ATP.14, GOL.21, FLC.22 11 PLIP interactions: 11 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:R.108, B:R.238 Salt bridges: B:K.103, B:K.103, B:R.238

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: R.15, Q.43, D.45, L.47, E.48, S.303, I.304 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.15, A:R.15, A:Q.43, A:E.48, A:E.48, A:I.304 GOL.4: 5 residues within 4Å: Chain A: F.218, S.221, R.291, T.293, R.310 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.215, A:F.218, A:S.221, A:R.310 GOL.5: 4 residues within 4Å: Chain A: L.125, T.127, Q.190 Ligands: FLC.9 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.127, A:T.127, A:Y.177 Water bridges: A:T.127, A:Q.190 GOL.6: 4 residues within 4Å: Chain A: Y.10, R.289, P.290, R.308 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.289, A:R.308 GOL.7: 8 residues within 4Å: Chain A: D.225, A.226, R.227, R.289, R.297, K.298, D.299, R.306 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.289, A:R.297, A:K.298, A:D.299, A:D.299 Water bridges: A:R.297, A:R.306 GOL.8: 4 residues within 4Å: Chain A: R.38, G.39, R.108 Ligands: ADP.2 1 PLIP interactions: 1 interactions with chain A Water bridges: A:L.40 GOL.16: 7 residues within 4Å: Chain B: R.15, Q.43, D.45, L.47, E.48, S.303, I.304 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.15, B:R.15, B:Q.43, B:E.48, B:E.48, B:E.48, B:I.304 GOL.17: 5 residues within 4Å: Chain B: F.218, S.221, R.291, T.293, R.310 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.215, B:F.218, B:S.221, B:R.310 GOL.18: 4 residues within 4Å: Chain B: L.125, T.127, Q.190 Ligands: FLC.22 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.127, B:Y.177 Water bridges: B:T.127, B:Q.190 GOL.19: 4 residues within 4Å: Chain B: Y.10, R.289, P.290, R.308 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.289, B:R.308 GOL.20: 8 residues within 4Å: Chain B: D.225, A.226, R.227, R.289, R.297, K.298, D.299, R.306 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.225, B:R.289, B:R.297, B:K.298, B:D.299 Water bridges: B:R.297, B:R.306 GOL.21: 4 residues within 4Å: Chain B: R.38, G.39, R.108 Ligands: ADP.15 1 PLIP interactions: 1 interactions with chain B Water bridges: B:L.40

2 x FLC: CITRATE ANION(Non-covalent)

FLC.9: 7 residues within 4Å: Chain A: Y.177, S.178, H.179, L.180 Ligands: ATP.1, ADP.2, GOL.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.177, A:Y.177, A:H.179, A:L.180 Salt bridges: A:H.179 FLC.22: 7 residues within 4Å: Chain B: Y.177, S.178, H.179, L.180 Ligands: ATP.14, ADP.15, GOL.18 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.177, B:Y.177, B:H.179, B:L.180 Salt bridges: B:H.179

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

NA.10: 5 residues within 4Å: Chain A: R.122, D.124, V.191, V.192, R.193 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.124, A:R.193 NA.23: 5 residues within 4Å: Chain B: R.122, D.124, V.191, V.192, R.193 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.124, B:R.193

6 x ACT: ACETATE ION(Non-functional Binders)

ACT.11: 1 residues within 4Å: Chain A: P.175 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.175 ACT.12: 2 residues within 4Å: Chain A: H.194, D.196 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.194 ACT.13: 7 residues within 4Å: Chain A: R.87, P.88, P.90, G.168, S.169, H.194, P.195 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:R.87, A:P.90, A:H.194 Hydrogen bonds: A:H.194 Salt bridges: A:R.87 ACT.24: 1 residues within 4Å: Chain B: P.175 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.175 ACT.25: 2 residues within 4Å: Chain B: H.194, D.196 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.194 ACT.26: 7 residues within 4Å: Chain B: R.87, P.88, P.90, G.168, S.169, H.194, P.195 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:R.87, B:P.90, B:H.194 Hydrogen bonds: B:H.194 Salt bridges: B:R.87

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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