SMTL ID : 2gev.1

Pantothenate kinase from Mycobacterium tuberculosis (MtPanK) in complex with a coenzyme A derivative, Form-II (LT)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

2 x COK: [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL (3R)-3-HYDROXY-4-{[3-({2-[(2-HYDROXYETHYL)DITHIO]ETHYL}AMINO)-3-OXOPROPYL]AMINO}-2,2-DIMETHYL-4-OXOBUTYL DIHYDROGEN DIPHOSPHATE(Non-covalent)

COK.1: 25 residues within 4Å: Chain A: G.39, L.40, 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: TRS.2 27 PLIP interactions: 27 interactions with chain A Hydrogen bonds: A:L.40, A:A.100, A:S.104, A:S.104, A:Y.182, A:Y.182, A:R.238, A:R.238, A:R.238, A:N.277, A:N.277 Water bridges: A:V.101, A:V.101, A:R.108, A:D.129, A:Y.177, A:Y.177, A:H.179, A:L.203, 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 COK.9: 25 residues within 4Å: Chain B: G.39, L.40, 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: TRS.10 26 PLIP interactions: 26 interactions with chain B Hydrogen bonds: B:L.40, B:A.100, B:S.104, B:S.104, B:D.129, B:Y.182, B:Y.235, B:R.238, B:R.238, B:R.238, B:N.277, B:N.277 Water bridges: B:V.101, B:V.101, B:T.105, B:D.129, B:H.179, B:L.203, 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

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.2: 5 residues within 4Å: Chain A: G.36, L.37, R.38, R.108 Ligands: COK.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.38 Water bridges: A:G.36, A:L.40, A:L.40 TRS.10: 5 residues within 4Å: Chain B: G.36, L.37, R.38, R.108 Ligands: COK.9 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.38 Water bridges: B:G.36, B:L.40, B:L.40

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: T.127, D.129, G.130, P.175, V.176, Y.177, H.179 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:T.127, A:D.129, A:P.175, A:Y.177, A:H.179 Water bridges: A:T.127, A:Y.177, A:Q.190, A:Q.190 GOL.4: 6 residues within 4Å: Chain A: R.15, Q.43, D.45, L.47, E.48, S.303 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.15, A:R.15, A:Q.43, A:S.303, A:I.304 GOL.5: 6 residues within 4Å: Chain A: S.215, F.218, S.221, R.291, T.293, R.310 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:F.218, A:S.221, A:S.221 Water bridges: A:F.218, A:F.218 GOL.6: 5 residues within 4Å: Chain A: C.173, G.187, A.188, E.189 Ligands: GOL.8 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.187, A:A.188, A:E.189 Water bridges: A:G.187, A:E.189 GOL.7: 5 residues within 4Å: Chain A: Q.111, A.115, P.121, R.122, V.123 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.111, A:V.123 GOL.8: 6 residues within 4Å: Chain A: R.160, F.161, S.164, A.172, C.173 Ligands: GOL.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.160, A:S.164 GOL.11: 7 residues within 4Å: Chain B: T.127, D.129, G.130, P.175, V.176, Y.177, H.179 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:T.127, B:P.175, B:Y.177, B:H.179 Water bridges: B:T.127, B:Q.190, B:Q.190 GOL.12: 6 residues within 4Å: Chain B: R.15, Q.43, D.45, L.47, E.48, S.303 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.15, B:R.15, B:Q.43, B:E.48, B:S.303, B:I.304 GOL.13: 6 residues within 4Å: Chain B: S.215, F.218, S.221, R.291, T.293, R.310 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:F.218, B:S.221, B:S.221 Water bridges: B:F.218, B:F.218 GOL.14: 5 residues within 4Å: Chain B: C.173, G.187, A.188, E.189 Ligands: GOL.16 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.187, B:A.188 Water bridges: B:G.187, B:E.189 GOL.15: 5 residues within 4Å: Chain B: Q.111, A.115, P.121, R.122, V.123 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.111, B:V.123 GOL.16: 6 residues within 4Å: Chain B: R.160, F.161, S.164, A.172, C.173 Ligands: GOL.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.160, B:S.164

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Das, S. et al., Invariance and variability in bacterial PanK: a study based on the crystal structure of Mycobacterium tuberculosis PanK. Acta Crystallogr.,Sect.D (2006)

Release Date

2006-06-06

Peptides

Pantothenate kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Pantothenate kinase

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