SMTL ID : 2zsa.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 15 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, F.254 Ligands: PAZ.2, GOL.6 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 Water bridges: A:G.102, A:K.103, A:K.103, A:R.108, A:H.179, A:R.238, A:R.238, A:R.238 Salt bridges: A:K.103, A:K.103, A:R.238, A:R.238 pi-Stacking: A:H.179 ADP.19: 15 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, F.254 Ligands: PAZ.20, GOL.24 19 PLIP interactions: 19 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 Water bridges: B:G.102, B:K.103, B:K.103, B:R.108, B:R.238, B:R.238, B:R.238 Salt bridges: B:K.103, B:K.103, B:R.238, 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: T.128, D.129, L.132, K.147, G.148, Y.153, H.179, G.202, L.203, Y.235, N.277 Ligands: ADP.1, GOL.6 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:D.129, A:L.132 Hydrogen bonds: A:T.128, A:T.128, A:T.128, A:T.128, A:D.129, A:L.203, A:N.277 PAZ.20: 13 residues within 4Å: Chain B: T.128, D.129, L.132, K.147, G.148, Y.153, H.179, G.202, L.203, Y.235, N.277 Ligands: ADP.19, GOL.24 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:D.129, B:L.132 Hydrogen bonds: B:T.128, B:T.128, B:T.128, B:D.129, B:Y.153, B:L.203, B:Y.235, B:N.277 Water bridges: B:T.128

22 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: Y.133, P.134, E.137, N.154 Ligand excluded by PLIP GOL.4: 4 residues within 4Å: Chain A: Y.177, S.178, H.179, L.180 Ligand excluded by PLIP GOL.5: 7 residues within 4Å: Chain A: F.218, D.219, F.220, S.221, R.291, T.293, R.310 Ligand excluded by PLIP GOL.6: 6 residues within 4Å: Chain A: Y.235, R.238, F.239, F.254 Ligands: ADP.1, PAZ.2 Ligand excluded by PLIP GOL.7: 3 residues within 4Å: Chain A: R.122, R.193, H.194 Ligand excluded by PLIP GOL.8: 8 residues within 4Å: Chain A: R.67, F.71, K.166, D.216, F.218, D.219 Chain B: R.310, L.312 Ligand excluded by PLIP GOL.9: 6 residues within 4Å: Chain A: R.15, Q.43, D.45, E.48, D.301, S.303 Ligand excluded by PLIP GOL.10: 3 residues within 4Å: Chain A: A.248, H.255, A.258 Ligand excluded by PLIP GOL.11: 3 residues within 4Å: Chain A: F.161, A.172, C.173 Ligand excluded by PLIP GOL.12: 4 residues within 4Å: Chain A: G.36, L.37, R.38, R.108 Ligand excluded by PLIP GOL.13: 4 residues within 4Å: Chain A: L.158, N.204, Q.207, M.213 Ligand excluded by PLIP GOL.21: 4 residues within 4Å: Chain B: Y.133, P.134, E.137, N.154 Ligand excluded by PLIP GOL.22: 4 residues within 4Å: Chain B: Y.177, S.178, H.179, L.180 Ligand excluded by PLIP GOL.23: 7 residues within 4Å: Chain B: F.218, D.219, F.220, S.221, R.291, T.293, R.310 Ligand excluded by PLIP GOL.24: 6 residues within 4Å: Chain B: Y.235, R.238, F.239, F.254 Ligands: ADP.19, PAZ.20 Ligand excluded by PLIP GOL.25: 3 residues within 4Å: Chain B: R.122, R.193, H.194 Ligand excluded by PLIP GOL.26: 8 residues within 4Å: Chain A: R.310, L.312 Chain B: R.67, F.71, K.166, D.216, F.218, D.219 Ligand excluded by PLIP GOL.27: 6 residues within 4Å: Chain B: R.15, Q.43, D.45, E.48, D.301, S.303 Ligand excluded by PLIP GOL.28: 3 residues within 4Å: Chain B: A.248, H.255, A.258 Ligand excluded by PLIP GOL.29: 3 residues within 4Å: Chain B: F.161, A.172, C.173 Ligand excluded by PLIP GOL.30: 4 residues within 4Å: Chain B: G.36, L.37, R.38, R.108 Ligand excluded by PLIP GOL.31: 4 residues within 4Å: Chain B: L.158, N.204, Q.207, M.213 Ligand excluded by PLIP

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

CL.14: 4 residues within 4Å: Chain A: T.208, P.287, R.291 Chain B: G.209 Ligand excluded by PLIP CL.32: 4 residues within 4Å: Chain A: G.209 Chain B: T.208, P.287, R.291 Ligand excluded by PLIP

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

NA.15: 3 residues within 4Å: Chain A: D.124, V.191, R.193 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.124, A:R.193 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.17: 4 residues within 4Å: Chain A: Y.223, D.225, L.281, L.286 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.223, A:Y.223, A:D.225 NA.18: 4 residues within 4Å: Chain A: R.146, F.149, E.283, N.284 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.146, A:E.283, A:N.284, A:N.284 Water bridges: A:R.146 NA.33: 3 residues within 4Å: Chain B: D.124, V.191, R.193 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.191, B:R.193 NA.34: 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:E.42 Water bridges: B:R.238 NA.35: 4 residues within 4Å: Chain B: Y.223, D.225, L.281, L.286 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.223 NA.36: 4 residues within 4Å: Chain B: R.146, F.149, E.283, N.284 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.146, B:E.283, B:N.284 Water bridges: B:R.146

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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