SMTL ID : 3avq.1

Pantothenate kinase from Mycobacterium tuberculosis (MtPanK) in complex with N9-Pan

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-dimer

Ligands

2 x MV1: (2S)-2,4-dihydroxy-3,3-dimethyl-N-[3-(nonylamino)-3-oxopropyl]butanamide(Non-covalent)

MV1.1: 12 residues within 4Å: Chain A: V.109, D.139, K.157, H.189, Y.192, Y.245, R.248, F.249, F.257, I.282, N.287 Ligands: FLC.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.109, A:Y.245, A:F.249, A:F.257, A:I.282, A:I.282 Hydrogen bonds: A:D.139, A:Y.187, A:Y.187, A:Y.192, A:Y.192, A:N.287 MV1.12: 12 residues within 4Å: Chain B: V.109, D.139, K.157, H.189, Y.192, Y.245, R.248, F.249, F.257, I.282, N.287 Ligands: FLC.13 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:V.109, B:Y.245, B:F.249, B:F.257, B:I.282, B:I.282 Hydrogen bonds: B:D.139, B:Y.187, B:Y.192, B:Y.245, B:N.287

2 x FLC: CITRATE ANION(Non-covalent)

FLC.2: 11 residues within 4Å: Chain A: E.52, V.109, A.110, V.111, G.112, K.113, S.114, T.115, R.118, R.248 Ligands: MV1.1 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:E.52, A:A.110, A:A.110, A:G.112, A:K.113, A:S.114, A:T.115, A:R.248 Salt bridges: A:K.113, A:K.113, A:R.118 FLC.13: 11 residues within 4Å: Chain B: E.52, V.109, A.110, V.111, G.112, K.113, S.114, T.115, R.118, R.248 Ligands: MV1.12 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:A.110, B:A.110, B:G.112, B:K.113, B:S.114, B:T.115, B:T.115, B:R.248 Salt bridges: B:K.113, B:K.113, B:R.118

18 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 1 residues within 4Å: Chain A: R.150 Ligand excluded by PLIP GOL.4: 4 residues within 4Å: Chain A: Y.187, S.188, H.189, L.190 Ligand excluded by PLIP GOL.5: 5 residues within 4Å: Chain A: A.167, R.170, F.171, A.182, C.183 Ligand excluded by PLIP GOL.6: 6 residues within 4Å: Chain A: L.135, V.136, T.137, P.185, Q.200 Ligands: GOL.11 Ligand excluded by PLIP GOL.7: 6 residues within 4Å: Chain A: D.235, A.236, R.237, R.307, K.308, R.316 Ligand excluded by PLIP GOL.8: 6 residues within 4Å: Chain A: S.225, F.228, S.231, R.301, T.303, R.320 Ligand excluded by PLIP GOL.9: 4 residues within 4Å: Chain A: C.183, P.185, A.198, E.199 Ligand excluded by PLIP GOL.10: 7 residues within 4Å: Chain A: R.25, Q.53, I.54, D.55, E.58, D.311, S.313 Ligand excluded by PLIP GOL.11: 4 residues within 4Å: Chain A: V.186, E.199, Q.200 Ligands: GOL.6 Ligand excluded by PLIP GOL.14: 1 residues within 4Å: Chain B: R.150 Ligand excluded by PLIP GOL.15: 4 residues within 4Å: Chain B: Y.187, S.188, H.189, L.190 Ligand excluded by PLIP GOL.16: 5 residues within 4Å: Chain B: A.167, R.170, F.171, A.182, C.183 Ligand excluded by PLIP GOL.17: 6 residues within 4Å: Chain B: L.135, V.136, T.137, P.185, Q.200 Ligands: GOL.22 Ligand excluded by PLIP GOL.18: 6 residues within 4Å: Chain B: D.235, A.236, R.237, R.307, K.308, R.316 Ligand excluded by PLIP GOL.19: 6 residues within 4Å: Chain B: S.225, F.228, S.231, R.301, T.303, R.320 Ligand excluded by PLIP GOL.20: 4 residues within 4Å: Chain B: C.183, P.185, A.198, E.199 Ligand excluded by PLIP GOL.21: 7 residues within 4Å: Chain B: R.25, Q.53, I.54, D.55, E.58, D.311, S.313 Ligand excluded by PLIP GOL.22: 4 residues within 4Å: Chain B: V.186, E.199, Q.200 Ligands: GOL.17 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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