SMTL ID : 2zse.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x ACP: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER(Non-covalent)

ACP.1: 15 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 Ligands: PAU.2, EDO.13 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:E.42, A:E.42, A:A.100, A:V.101, A:G.102, A:K.103, A:K.103, A:K.103, A:S.104, A:S.104, A:T.105, A:R.108, A:R.108, A:R.238 Water bridges: A:S.104, A:E.201 Salt bridges: A:R.108, A:R.238 pi-Stacking: A:H.179, A:H.179 ACP.18: 15 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 Ligands: PAU.19, EDO.30 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:E.42, B:A.100, B:V.101, B:G.102, B:K.103, B:K.103, B:K.103, B:S.104, B:S.104, B:T.105, B:T.105, B:R.108, B:R.108, B:R.238 Water bridges: B:S.104, B:E.201 Salt bridges: B:R.108, B:R.238 pi-Stacking: B:H.179, B:H.179

2 x PAU: PANTOTHENOIC ACID(Non-covalent)

PAU.2: 9 residues within 4Å: Chain A: Y.235, R.238, F.239, M.242, F.247, I.272, N.277 Ligands: ACP.1, EDO.10 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.235, A:R.238, A:F.239 Hydrogen bonds: A:R.238, A:R.238, A:N.277 PAU.19: 9 residues within 4Å: Chain B: Y.235, R.238, F.239, M.242, F.247, I.272, N.277 Ligands: ACP.18, EDO.27 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.235, B:R.238, B:F.239 Hydrogen bonds: B:Y.235, B:R.238, B:R.238, B:N.277

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: R.69, A.72, A.73, E.76 Chain B: A.66 No protein-ligand interaction detected (PLIP) GOL.4: 4 residues within 4Å: Chain A: L.286, R.289, P.290, R.308 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.289, A:R.289, A:R.308, A:R.308 GOL.5: 2 residues within 4Å: Chain A: R.146, E.283 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.146, A:R.146 Water bridges: A:T.275, A:E.283, A:E.283, A:E.283 GOL.6: 3 residues within 4Å: Chain A: D.183, I.184, P.186 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.183 GOL.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.8: 6 residues within 4Å: Chain A: Y.177, S.178, H.179, L.180, I.185 Ligands: EDO.14 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.179, A:L.180 GOL.20: 5 residues within 4Å: Chain A: A.66 Chain B: R.69, A.72, A.73, E.76 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.76 GOL.21: 4 residues within 4Å: Chain B: L.286, R.289, P.290, R.308 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.289, B:R.289, B:R.308, B:R.308 GOL.22: 2 residues within 4Å: Chain B: R.146, E.283 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.146, B:R.146 Water bridges: B:T.275, B:E.283, B:E.283 GOL.23: 3 residues within 4Å: Chain B: D.183, I.184, P.186 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.183, B:D.183 GOL.24: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) GOL.25: 6 residues within 4Å: Chain B: Y.177, S.178, H.179, L.180, I.185 Ligands: EDO.31 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.179, B:L.180

12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.9: 5 residues within 4Å: Chain A: R.15, Q.43, D.45, E.48, S.303 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.15, A:R.15, A:Q.43, A:E.48 EDO.10: 4 residues within 4Å: Chain A: K.147, Y.182, N.277 Ligands: PAU.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.182, A:N.277 EDO.11: 5 residues within 4Å: Chain A: L.125, V.126, T.127, Q.190 Ligands: EDO.14 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.127, A:T.127, A:Q.190 EDO.12: 4 residues within 4Å: Chain A: S.263, V.266, V.267, R.270 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.263 EDO.13: 6 residues within 4Å: Chain A: G.36, L.37, R.38, G.39, R.108 Ligands: ACP.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.108 Water bridges: A:L.40 EDO.14: 8 residues within 4Å: Chain A: T.127, D.129, G.130, V.176, Y.177, H.179 Ligands: GOL.8, EDO.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.130, A:Y.177, A:H.179 EDO.26: 5 residues within 4Å: Chain B: R.15, Q.43, D.45, E.48, S.303 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.15, B:R.15, B:Q.43, B:E.48 EDO.27: 4 residues within 4Å: Chain B: K.147, Y.182, N.277 Ligands: PAU.19 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.277 EDO.28: 5 residues within 4Å: Chain B: L.125, V.126, T.127, Q.190 Ligands: EDO.31 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.127, B:T.127, B:Q.190 Water bridges: B:T.127 EDO.29: 4 residues within 4Å: Chain B: S.263, V.266, V.267, R.270 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.263 EDO.30: 6 residues within 4Å: Chain B: G.36, L.37, R.38, G.39, R.108 Ligands: ACP.18 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.108 Water bridges: B:L.40 EDO.31: 8 residues within 4Å: Chain B: T.127, D.129, G.130, V.176, Y.177, H.179 Ligands: GOL.25, EDO.28 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.130, B:Y.177, B:H.179

2 x FLC: CITRATE ANION(Non-covalent)

FLC.15: 3 residues within 4Å: Chain A: R.122, R.193, H.194 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.122, A:R.122 Salt bridges: A:R.122, A:R.122, A:R.193, A:H.194, A:H.194 FLC.32: 3 residues within 4Å: Chain B: R.122, R.193, H.194 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.122, B:R.122 Salt bridges: B:R.122, B:R.122, B:R.193, B:H.194, B:H.194

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

NA.16: 3 residues within 4Å: Chain A: R.122, D.124, R.193 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.124, A:R.193 NA.17: 3 residues within 4Å: Chain A: L.312 Chain B: K.166, D.216 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:L.312, B:K.166, B:K.166 NA.33: 3 residues within 4Å: Chain B: R.122, D.124, R.193 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.191, B:R.193 NA.34: 3 residues within 4Å: Chain A: K.166, D.216 Chain B: L.312 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:L.312, A:K.166

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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