SMTL ID : 5wdg.1

Acetolactate Synthase from Klebsiella pneumoniae in Complex with a Reaction Intermediate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.12 Å

Oligo State

homo-tetramer

Ligands

12 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 8 residues within 4Å: Chain A: D.467, G.468, D.494, G.496, Y.497, N.498, F.516 Ligands: A4Y.5 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.467, A:D.494, A:G.496, H2O.2 MG.2: 3 residues within 4Å: Chain A: R.89, Q.240, P.241 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:R.89, H2O.6, H2O.7 MG.3: 2 residues within 4Å: Chain A: S.149, T.152 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:S.149, A:T.152, H2O.4, H2O.6, H2O.7, H2O.8 MG.7: 8 residues within 4Å: Chain B: D.467, G.468, D.494, G.496, Y.497, N.498, F.516 Ligands: A4Y.11 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.467, B:D.494, B:G.496, H2O.11 MG.8: 2 residues within 4Å: Chain B: S.149, T.152 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:S.149, B:T.152, H2O.14, H2O.16 MG.9: 6 residues within 4Å: Chain B: L.64, L.65, S.67, I.69, R.70, I.71 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:L.64, B:S.67, B:I.69, H2O.17 MG.13: 8 residues within 4Å: Chain C: D.467, G.468, D.494, G.496, Y.497, N.498, F.516 Ligands: A4Y.17 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.467, C:D.494, C:G.496, H2O.21 MG.14: 3 residues within 4Å: Chain C: R.89, Q.240, P.241 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:R.89, H2O.25, H2O.26 MG.15: 2 residues within 4Å: Chain C: S.149, T.152 6 PLIP interactions: 2 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:S.149, C:T.152, H2O.24, H2O.25, H2O.27, H2O.27 MG.19: 8 residues within 4Å: Chain D: D.467, G.468, D.494, G.496, Y.497, N.498, F.516 Ligands: A4Y.23 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.467, D:D.494, D:G.496, H2O.30 MG.20: 2 residues within 4Å: Chain D: S.149, T.152 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:S.149, D:T.152, H2O.33, H2O.35 MG.21: 6 residues within 4Å: Chain D: L.64, L.65, S.67, I.69, R.70, I.71 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:L.64, D:S.67, D:I.69, H2O.36

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.4: 9 residues within 4Å: Chain A: F.276, G.278, R.279, Q.286, R.372, A.422, R.423, L.425, Y.426 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.279, A:R.279, A:Q.286, A:R.423, A:L.425, A:Y.426 Salt bridges: A:R.279, A:R.372 PO4.10: 8 residues within 4Å: Chain B: F.276, G.278, R.279, Q.286, R.372, A.422, L.425, Y.426 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:R.279, B:R.279, B:Q.286, B:L.425, B:Y.426 Salt bridges: B:R.279, B:R.372 PO4.16: 9 residues within 4Å: Chain C: F.276, G.278, R.279, Q.286, R.372, A.422, R.423, L.425, Y.426 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:R.279, C:R.279, C:Q.286, C:R.423, C:L.425, C:Y.426 Salt bridges: C:R.279, C:R.372 PO4.22: 8 residues within 4Å: Chain D: F.276, G.278, R.279, Q.286, R.372, A.422, L.425, Y.426 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:R.279, D:R.279, D:Q.286, D:L.425, D:Y.426 Salt bridges: D:R.279, D:R.372

4 x A4Y: (2S,3S)-2,3-dihydroxy-3-[(7S,8R,9aS)-8-(2-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-2,7-dimethyl-5,7,8,10-tetrahydro-9aH-pyrimido[4,5-d][1,3]thiazolo[3,2-a]pyrimidin-9a-yl]-2-methylbutanoic acid(Non-covalent)

A4Y.5: 31 residues within 4Å: Chain A: M.414, G.415, S.416, F.417, Q.440, T.441, M.442, G.466, D.467, G.468, G.469, Q.472, W.492, D.494, G.496, Y.497, N.498, M.499, V.500, F.516, Y.563 Chain C: I.52, P.53, G.54, A.55, E.77, T.100, P.103, G.104, N.107 Ligands: MG.1 20 PLIP interactions: 16 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: A:Q.440, A:Y.497, C:P.103 Hydrogen bonds: A:S.416, A:Q.440, A:Q.440, A:M.442, A:G.466, A:D.467, A:D.467, A:G.468, A:G.469, A:N.498, A:M.499, A:Y.563, C:A.55 Water bridges: A:M.414, A:G.466, C:K.56, C:T.100 A4Y.11: 31 residues within 4Å: Chain B: M.414, G.415, S.416, F.417, Q.440, T.441, M.442, G.466, D.467, G.468, G.469, Q.472, D.494, G.496, Y.497, N.498, M.499, V.500, F.516, Y.563 Chain D: I.52, P.53, G.54, A.55, E.77, T.100, P.103, G.104, N.107, Q.140 Ligands: MG.7 25 PLIP interactions: 17 interactions with chain B, 8 interactions with chain D Hydrophobic interactions: B:Q.440, B:M.442, B:Y.497, B:V.500, D:I.52, D:T.100, D:P.103 Hydrogen bonds: B:S.416, B:Q.440, B:Q.440, B:Q.440, B:M.442, B:G.466, B:D.467, B:D.467, B:G.468, B:G.469, B:N.498, B:M.499, B:Y.563, D:A.55 Water bridges: D:K.56, D:T.100, D:Q.140 Salt bridges: D:K.56 A4Y.17: 31 residues within 4Å: Chain A: I.52, P.53, G.54, A.55, E.77, T.100, P.103, G.104, N.107 Chain C: M.414, G.415, S.416, F.417, Q.440, T.441, M.442, G.466, D.467, G.468, G.469, Q.472, W.492, D.494, G.496, Y.497, N.498, M.499, V.500, F.516, Y.563 Ligands: MG.13 21 PLIP interactions: 5 interactions with chain A, 16 interactions with chain C Hydrophobic interactions: A:P.103, C:Q.440, C:Y.497 Hydrogen bonds: A:A.55, C:S.416, C:Q.440, C:Q.440, C:M.442, C:G.466, C:D.467, C:D.467, C:G.468, C:G.469, C:N.498, C:M.499, C:Y.563 Water bridges: A:K.56, A:E.77, A:T.100, C:M.414, C:G.466 A4Y.23: 31 residues within 4Å: Chain B: I.52, P.53, G.54, A.55, E.77, T.100, P.103, G.104, N.107, Q.140 Chain D: M.414, G.415, S.416, F.417, Q.440, T.441, M.442, G.466, D.467, G.468, G.469, Q.472, D.494, G.496, Y.497, N.498, M.499, V.500, F.516, Y.563 Ligands: MG.19 25 PLIP interactions: 9 interactions with chain B, 16 interactions with chain D Hydrophobic interactions: B:I.52, B:T.100, B:P.103, D:Q.440, D:M.442, D:Y.497, D:V.500 Hydrogen bonds: B:A.55, D:S.416, D:Q.440, D:Q.440, D:Q.440, D:M.442, D:G.466, D:D.467, D:G.468, D:G.469, D:N.498, D:M.499, D:Y.563 Water bridges: B:K.56, B:E.77, B:T.100, B:Q.140 Salt bridges: B:K.56

4 x PYR: PYRUVIC ACID(Non-covalent)

PYR.6: 10 residues within 4Å: Chain A: S.117, E.118, G.119, R.179, P.180, L.236, Q.263, S.304, V.306, E.307 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.179, A:Q.263 Salt bridges: A:R.179 PYR.12: 3 residues within 4Å: Chain B: Y.508, Q.509, R.510 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.508 Water bridges: B:R.510 PYR.18: 10 residues within 4Å: Chain C: S.117, E.118, G.119, R.179, P.180, L.236, Q.263, S.304, V.306, E.307 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.179, C:Q.263 Salt bridges: C:R.179 PYR.24: 3 residues within 4Å: Chain D: Y.508, Q.509, R.510 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.508 Water bridges: D:R.510

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Latta, A.J. et al., Acetolactate Synthase from Klebsiella pneumoniae in Complex with Mechanism-Based Inhibitor. To Be Published

Release Date

2018-07-11

Peptides

Acetolactate synthase, catabolic: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Acetolactate synthase, catabolic

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