SMTL ID : 2zsd.1

Pantothenate kinase from Mycobacterium tuberculosis (MtPanK) in complex with Coenzyme A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

4 x COA: COENZYME A(Non-covalent)

COA.1: 25 residues within 4Å: Chain A: G.39, V.99, A.100, K.103, S.104, R.108, D.129, K.147, G.148, Y.177, H.179, Y.182, L.203, Y.235, R.238, F.239, M.242, A.246, F.247, F.254, I.272, I.276, N.277 Ligands: GOL.5, EDO.9 27 PLIP interactions: 27 interactions with chain A Hydrogen bonds: A:A.100, A:S.104, A:S.104, A:Y.182, A:Y.182, A:R.238, A:N.277, A:N.277 Water bridges: A:L.40, A:G.102, A:G.102, A:S.104, A:R.108, A:D.129, A:Y.177, A:H.179, A:E.201, A:L.203, A:R.238, A:R.238, A:R.238 Salt bridges: A:K.103, A:K.103, A:R.108, A:H.179, A:R.238 pi-Stacking: A:H.179 COA.2: 8 residues within 4Å: Chain A: E.12, F.13, R.289, V.295, R.297, R.306, L.307, R.308 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.306, A:L.307, A:L.307 Water bridges: A:R.289, A:R.297, A:R.297, A:R.308 Salt bridges: A:R.289, A:R.297 pi-Cation interactions: A:R.306 COA.14: 25 residues within 4Å: Chain B: G.39, V.99, A.100, K.103, S.104, R.108, D.129, K.147, G.148, Y.177, H.179, Y.182, L.203, Y.235, R.238, F.239, M.242, A.246, F.247, F.254, I.272, I.276, N.277 Ligands: GOL.18, EDO.22 27 PLIP interactions: 27 interactions with chain B Hydrogen bonds: B:A.100, B:S.104, B:S.104, B:Y.182, B:Y.235, B:R.238, B:N.277, B:N.277 Water bridges: B:L.40, B:G.102, B:G.102, B:S.104, B:T.105, B:D.129, B:Y.153, B:H.179, B:E.201, B:L.203, B:R.238, B:R.238, B:R.238 Salt bridges: B:K.103, B:K.103, B:R.108, B:H.179, B:R.238 pi-Stacking: B:H.179 COA.15: 8 residues within 4Å: Chain B: E.12, F.13, R.289, V.295, R.297, R.306, L.307, R.308 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:R.306, B:L.307, B:L.307 Water bridges: B:R.289, B:R.297, B:R.297, B:R.308 Salt bridges: B:R.289, B:R.297 pi-Cation interactions: B:R.306

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: Q.207, T.208, P.287, T.288, R.291 Chain B: G.209, P.210 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.208, A:T.208, A:P.287, A:R.291, A:R.291 GOL.4: 4 residues within 4Å: Chain A: Y.177, S.178, H.179, L.180 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.177, A:H.179, A:H.179, A:L.180 GOL.5: 6 residues within 4Å: Chain A: V.99, Y.235, R.238, F.239, M.242 Ligands: COA.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.235, A:R.238 GOL.6: 5 residues within 4Å: Chain A: D.86, H.119, R.122, H.194, D.196 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.119, A:H.194 GOL.7: 1 residues within 4Å: Chain A: H.256 No protein-ligand interaction detected (PLIP) GOL.16: 7 residues within 4Å: Chain A: G.209, P.210 Chain B: Q.207, T.208, P.287, T.288, R.291 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.208, B:T.208, B:P.287, B:R.291, B:R.291 GOL.17: 4 residues within 4Å: Chain B: Y.177, S.178, H.179, L.180 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.177, B:H.179, B:L.180 GOL.18: 6 residues within 4Å: Chain B: V.99, Y.235, R.238, F.239, M.242 Ligands: COA.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.235, B:R.238 GOL.19: 5 residues within 4Å: Chain B: D.86, H.119, R.122, H.194, D.196 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.119, B:H.194 GOL.20: 1 residues within 4Å: Chain B: H.256 No protein-ligand interaction detected (PLIP)

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

EDO.8: 9 residues within 4Å: Chain A: E.42, I.44, E.48, Y.53, G.102, T.105, T.106, K.298, I.304 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.48, A:Y.53, A:G.102, A:T.106, A:K.298 EDO.9: 5 residues within 4Å: Chain A: G.36, R.38, G.39, R.108 Ligands: COA.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.38 Water bridges: A:L.40 EDO.10: 3 residues within 4Å: Chain A: P.175, G.187, A.188 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.187 EDO.11: 3 residues within 4Å: Chain A: R.122, R.193, H.194 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.122, A:R.122 EDO.12: 5 residues within 4Å: Chain A: Q.139, N.142, L.143, M.144, H.145 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.144, A:H.145 Water bridges: A:Q.139, A:H.145 EDO.21: 9 residues within 4Å: Chain B: E.42, I.44, E.48, Y.53, G.102, T.105, T.106, K.298, I.304 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.48, B:G.102, B:K.298 Water bridges: B:E.42 EDO.22: 5 residues within 4Å: Chain B: G.36, R.38, G.39, R.108 Ligands: COA.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.38 Water bridges: B:L.40 EDO.23: 3 residues within 4Å: Chain B: P.175, G.187, A.188 1 PLIP interactions: 1 interactions with chain B Water bridges: B:G.187 EDO.24: 3 residues within 4Å: Chain B: R.122, R.193, H.194 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.122, B:R.122 EDO.25: 5 residues within 4Å: Chain B: Q.139, N.142, L.143, M.144, H.145 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:M.144, B:H.145 Water bridges: B:Q.139, B:H.145

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

NA.13: 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.26: 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:V.191, B:R.193

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

Related Entries With Identical Sequence