SMTL ID : 4tsk.1

Ketol-acid reductoisomerase from Alicyclobacillus acidocaldarius

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

12 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 6 residues within 4Å: Chain A: R.247, Y.248, I.250, S.251, D.252, Q.255 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:R.247, A:I.250, A:D.252, H2O.1 MG.2: 4 residues within 4Å: Chain A: D.190, E.194 Chain D: E.226 Ligands: TLA.4 4 PLIP interactions: 1 interactions with chain D, 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: D:E.226, A:D.190, A:D.190, H2O.6 MG.3: 3 residues within 4Å: Chain A: D.190, E.194 Ligands: TLA.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.190, A:E.194, H2O.1, H2O.1 MG.6: 6 residues within 4Å: Chain B: R.247, Y.248, I.250, S.251, D.252, Q.255 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:R.247, B:I.250, B:D.252, H2O.3 MG.7: 4 residues within 4Å: Chain B: D.190, E.194 Chain C: E.226 Ligands: TLA.9 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: B:D.190, B:D.190, C:E.226, H2O.4 MG.8: 3 residues within 4Å: Chain B: D.190, E.194 Ligands: TLA.9 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.190, B:E.194, H2O.3, H2O.3 MG.11: 6 residues within 4Å: Chain C: R.247, Y.248, I.250, S.251, D.252, Q.255 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:R.247, C:I.250, C:D.252, H2O.5 MG.12: 4 residues within 4Å: Chain B: E.226 Chain C: D.190, E.194 Ligands: TLA.14 4 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: B:E.226, C:D.190, C:D.190, H2O.2 MG.13: 3 residues within 4Å: Chain C: D.190, E.194 Ligands: TLA.14 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.190, C:E.194, H2O.4, H2O.5 MG.16: 6 residues within 4Å: Chain D: R.247, Y.248, I.250, S.251, D.252, Q.255 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:R.247, D:I.250, D:D.252, H2O.7 MG.17: 4 residues within 4Å: Chain A: E.226 Chain D: D.190, E.194 Ligands: TLA.19 4 PLIP interactions: 1 interactions with chain A, 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: A:E.226, D:D.190, D:D.190, H2O.1 MG.18: 3 residues within 4Å: Chain D: D.190, E.194 Ligands: TLA.19 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.190, D:E.194, H2O.6, H2O.7

4 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.4: 12 residues within 4Å: Chain A: G.131, P.132, D.190, E.194, L.198 Chain D: E.230, I.250, S.251, A.254 Ligands: MG.2, MG.3, NDP.5 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:G.131, D:S.251 Water bridges: A:H.107, A:K.130, A:K.130, D:S.251 TLA.9: 12 residues within 4Å: Chain B: G.131, P.132, D.190, E.194, L.198 Chain C: E.230, I.250, S.251, A.254 Ligands: MG.7, MG.8, NDP.10 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:G.131, C:S.251 Water bridges: B:H.107, B:K.130, B:K.130, C:S.251 TLA.14: 12 residues within 4Å: Chain B: E.230, I.250, S.251, A.254 Chain C: G.131, P.132, D.190, E.194, L.198 Ligands: MG.12, MG.13, NDP.15 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:G.131, C:E.194, B:S.251 Water bridges: C:H.107, C:K.130, C:K.130, B:S.251 TLA.19: 12 residues within 4Å: Chain A: E.230, I.250, S.251, A.254 Chain D: G.131, P.132, D.190, E.194, L.198 Ligands: MG.17, MG.18, NDP.20 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:G.131, D:E.194, A:S.251 Water bridges: D:H.107, D:K.130, D:K.130, A:S.251

4 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.5: 25 residues within 4Å: Chain A: G.24, Y.25, G.26, S.27, Q.28, L.47, R.48, S.52, V.66, L.79, L.80, P.81, D.82, Q.85, V.88, A.106, H.107, P.129, G.131, P.132, G.133 Chain D: S.249, I.250, S.251 Ligands: TLA.4 24 PLIP interactions: 20 interactions with chain A, 4 interactions with chain D Hydrophobic interactions: A:Q.28 Hydrogen bonds: A:Y.25, A:Y.25, A:S.27, A:S.27, A:Q.28, A:Q.28, A:R.48, A:S.52, A:S.52, A:S.52, A:L.80, A:D.82, A:Q.85, A:G.133, D:S.249 Water bridges: A:G.26, A:G.29, A:H.107, D:S.249, D:I.250, D:D.252 Salt bridges: A:R.48 pi-Cation interactions: A:R.48 NDP.10: 25 residues within 4Å: Chain B: G.24, Y.25, G.26, S.27, Q.28, L.47, R.48, S.52, V.66, L.79, L.80, P.81, D.82, Q.85, V.88, A.106, H.107, P.129, G.131, P.132, G.133 Chain C: S.249, I.250, S.251 Ligands: TLA.9 24 PLIP interactions: 4 interactions with chain C, 20 interactions with chain B Hydrogen bonds: C:S.249, B:Y.25, B:Y.25, B:S.27, B:S.27, B:Q.28, B:Q.28, B:R.48, B:S.52, B:S.52, B:S.52, B:L.80, B:D.82, B:Q.85, B:G.133 Water bridges: C:S.249, C:I.250, C:D.252, B:G.26, B:G.29, B:H.107 Hydrophobic interactions: B:Q.28 Salt bridges: B:R.48 pi-Cation interactions: B:R.48 NDP.15: 25 residues within 4Å: Chain B: S.249, I.250, S.251 Chain C: G.24, Y.25, G.26, S.27, Q.28, L.47, R.48, S.52, V.66, L.79, L.80, P.81, D.82, Q.85, V.88, A.106, H.107, P.129, G.131, P.132, G.133 Ligands: TLA.14 24 PLIP interactions: 20 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:Q.28 Hydrogen bonds: C:Y.25, C:Y.25, C:S.27, C:S.27, C:Q.28, C:Q.28, C:R.48, C:S.52, C:S.52, C:S.52, C:L.80, C:D.82, C:Q.85, C:G.133, B:S.249 Water bridges: C:G.26, C:G.29, C:H.107, B:S.249, B:I.250, B:D.252 Salt bridges: C:R.48 pi-Cation interactions: C:R.48 NDP.20: 25 residues within 4Å: Chain A: S.249, I.250, S.251 Chain D: G.24, Y.25, G.26, S.27, Q.28, L.47, R.48, S.52, V.66, L.79, L.80, P.81, D.82, Q.85, V.88, A.106, H.107, P.129, G.131, P.132, G.133 Ligands: TLA.19 24 PLIP interactions: 20 interactions with chain D, 4 interactions with chain A Hydrophobic interactions: D:Q.28 Hydrogen bonds: D:Y.25, D:Y.25, D:S.27, D:S.27, D:Q.28, D:Q.28, D:R.48, D:S.52, D:S.52, D:S.52, D:L.80, D:D.82, D:Q.85, D:G.133, A:S.249 Water bridges: D:G.26, D:G.29, D:H.107, A:S.249, A:I.250, A:D.252 Salt bridges: D:R.48 pi-Cation interactions: D:R.48

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brinkmann-Chen, S. et al., Uncovering rare NADH-preferring ketol-acid reductoisomerases. Metab. Eng. (2014)

Release Date

2014-07-09

Peptides

Ketol-acid reductoisomerase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Ketol-acid reductoisomerase