SMTL ID : 3avp.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

2 x MV2: (2S)-2,4-dihydroxy-N-(3-hydroxypropyl)-3,3-dimethylbutanamide(Non-covalent)

MV2.1: 11 residues within 4Å: Chain A: V.99, D.129, K.147, Y.177, H.179, Y.182, L.203, Y.235, I.272, N.277 Ligands: GOL.15 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.99, A:L.203, A:I.272 Hydrogen bonds: A:H.179, A:Y.235, A:N.277 MV2.16: 11 residues within 4Å: Chain B: V.99, D.129, K.147, Y.177, H.179, Y.182, L.203, Y.235, I.272, N.277 Ligands: GOL.30 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:V.99, B:L.203, B:I.272 Hydrogen bonds: B:H.179, B:N.277

2 x FLC: CITRATE ANION(Non-covalent)

FLC.2: 12 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, R.238 Ligands: NA.3 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:A.100, A:V.101, A:G.102, A:G.102, A:K.103, A:S.104, A:S.104, A:T.105, A:T.105 Water bridges: A:L.40, A:R.108 Salt bridges: A:K.103, A:K.103, A:R.108, A:R.238 FLC.17: 12 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, R.238 Ligands: NA.18 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:A.100, B:V.101, B:G.102, B:G.102, B:K.103, B:S.104, B:S.104, B:T.105 Water bridges: B:L.40, B:R.108 Salt bridges: B:K.103, B:K.103, B:R.108, B:R.238

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

NA.3: 4 residues within 4Å: Chain A: G.39, R.108 Ligands: FLC.2, GOL.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.108 Water bridges: A:R.108 NA.4: 4 residues within 4Å: Chain A: A.157, R.160, F.161 Ligands: GOL.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.160, A:F.161 Water bridges: A:C.173 NA.18: 4 residues within 4Å: Chain B: G.39, R.108 Ligands: FLC.17, GOL.24 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.108 Water bridges: B:R.108 NA.19: 4 residues within 4Å: Chain B: A.157, R.160, F.161 Ligands: GOL.21 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.157, B:R.160, B:F.161

22 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 10 residues within 4Å: Chain A: L.206, S.215, F.218, D.219, F.220, S.221, R.291, T.293, R.310 Ligands: GOL.13 Ligand excluded by PLIP GOL.6: 5 residues within 4Å: Chain A: F.161, S.164, A.172, C.173 Ligands: NA.4 Ligand excluded by PLIP GOL.7: 6 residues within 4Å: Chain A: R.15, Q.43, D.45, E.48, S.303, I.304 Ligand excluded by PLIP GOL.8: 5 residues within 4Å: Chain A: R.122, D.124, V.191, V.192, R.193 Ligand excluded by PLIP GOL.9: 5 residues within 4Å: Chain A: G.36, R.38, G.39, R.108 Ligands: NA.3 Ligand excluded by PLIP GOL.10: 4 residues within 4Å: Chain A: Y.177, S.178, H.179, L.180 Ligand excluded by PLIP GOL.11: 2 residues within 4Å: Chain A: P.175, A.188 Ligand excluded by PLIP GOL.12: 3 residues within 4Å: Chain A: V.176, E.189, Q.190 Ligand excluded by PLIP GOL.13: 9 residues within 4Å: Chain A: Q.63, R.67, T.293, R.310, K.311, L.312 Chain B: L.70, T.74 Ligands: GOL.5 Ligand excluded by PLIP GOL.14: 4 residues within 4Å: Chain A: R.146, T.275, P.279, E.283 Ligand excluded by PLIP GOL.15: 5 residues within 4Å: Chain A: Y.235, F.239, F.247, F.254 Ligands: MV2.1 Ligand excluded by PLIP GOL.20: 10 residues within 4Å: Chain B: L.206, S.215, F.218, D.219, F.220, S.221, R.291, T.293, R.310 Ligands: GOL.28 Ligand excluded by PLIP GOL.21: 5 residues within 4Å: Chain B: F.161, S.164, A.172, C.173 Ligands: NA.19 Ligand excluded by PLIP GOL.22: 6 residues within 4Å: Chain B: R.15, Q.43, D.45, E.48, S.303, I.304 Ligand excluded by PLIP GOL.23: 5 residues within 4Å: Chain B: R.122, D.124, V.191, V.192, R.193 Ligand excluded by PLIP GOL.24: 5 residues within 4Å: Chain B: G.36, R.38, G.39, R.108 Ligands: NA.18 Ligand excluded by PLIP GOL.25: 4 residues within 4Å: Chain B: Y.177, S.178, H.179, L.180 Ligand excluded by PLIP GOL.26: 2 residues within 4Å: Chain B: P.175, A.188 Ligand excluded by PLIP GOL.27: 3 residues within 4Å: Chain B: V.176, E.189, Q.190 Ligand excluded by PLIP GOL.28: 9 residues within 4Å: Chain A: L.70, T.74 Chain B: Q.63, R.67, T.293, R.310, K.311, L.312 Ligands: GOL.20 Ligand excluded by PLIP GOL.29: 4 residues within 4Å: Chain B: R.146, T.275, P.279, E.283 Ligand excluded by PLIP GOL.30: 5 residues within 4Å: Chain B: Y.235, F.239, F.247, F.254 Ligands: MV2.16 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chetnani, B. et al., Location and conformation of pantothenate and its derivatives in Mycobacterium tuberculosis pantothenate kinase: insights into enzyme action. Acta Crystallogr.,Sect.D (2011)

Release Date

2011-08-17

Peptides

Pantothenate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Pantothenate kinase

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