SMTL ID : 4kqx.1

Mutant Slackia exigua KARI DDV in complex with NAD and an inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 27 residues within 4Å: Chain A: G.34, Y.35, G.36, S.37, Q.38, L.57, R.58, D.61, M.77, L.90, V.91, P.92, D.93, V.95, Q.96, V.99, A.117, H.118, P.140, G.142, P.143, G.144 Chain B: S.260, I.261, S.262 Ligands: HIO.7, MG.12 24 PLIP interactions: 4 interactions with chain B, 20 interactions with chain A Hydrogen bonds: B:S.262, A:Y.35, A:Y.35, A:S.37, A:S.37, A:Q.38, A:Q.38, A:R.58, A:D.93, A:Q.96, A:G.142, A:G.144 Water bridges: B:N.263, B:N.263, B:N.263, A:G.36, A:G.36, A:D.61, A:D.61, A:D.61, A:H.118 Hydrophobic interactions: A:Q.38 pi-Cation interactions: A:R.58, A:R.58 NAD.8: 28 residues within 4Å: Chain A: S.260, I.261, S.262 Chain B: G.34, Y.35, G.36, S.37, Q.38, L.57, R.58, D.61, M.77, L.90, V.91, P.92, D.93, V.95, Q.96, V.99, A.117, H.118, P.140, G.142, P.143, G.144 Ligands: HIO.2, MG.4, MG.14 21 PLIP interactions: 2 interactions with chain A, 19 interactions with chain B Hydrogen bonds: A:S.262, B:Y.35, B:Y.35, B:S.37, B:S.37, B:Q.38, B:Q.38, B:R.58, B:D.93, B:Q.96, B:G.142, B:G.144 Water bridges: A:N.263, B:R.58, B:D.61, B:D.61, B:H.118, B:N.121 Hydrophobic interactions: B:Q.38 pi-Cation interactions: B:R.58, B:R.58

2 x HIO: N-HYDROXY-N-ISOPROPYLOXAMIC ACID(Non-covalent)

HIO.2: 13 residues within 4Å: Chain A: E.241, I.245, I.261, S.262, A.265 Chain B: G.142, P.143, D.201, E.205, C.210 Ligands: NAD.8, MG.13, MG.15 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:P.143, A:I.245, A:I.261 Water bridges: B:P.140, B:K.141, B:K.141, B:D.201, A:E.241, A:S.262, A:S.262 HIO.7: 12 residues within 4Å: Chain A: P.143, D.201, E.205, C.210 Chain B: E.241, I.245, I.261, S.262, A.265 Ligands: NAD.1, MG.5, MG.6 9 PLIP interactions: 1 interactions with chain B, 8 interactions with chain A Water bridges: B:S.262, A:H.118, A:K.141, A:K.141, A:K.141 Hydrophobic interactions: A:P.143, A:E.205 Hydrogen bonds: A:E.205, A:E.205

10 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: N.258, Y.259, I.261, S.262, N.263, E.266 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:N.258, A:I.261, A:E.266 MG.4: 5 residues within 4Å: Chain A: Y.259, S.260, I.261 Chain B: S.37 Ligands: NAD.8 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:Y.259, A:S.260, A:I.261, H2O.4 MG.5: 4 residues within 4Å: Chain A: K.141, D.201 Ligands: MG.6, HIO.7 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.201, H2O.4, H2O.10, H2O.10 MG.6: 4 residues within 4Å: Chain A: D.201, E.205 Ligands: MG.5, HIO.7 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.201, A:E.205, H2O.5, H2O.10 MG.10: 6 residues within 4Å: Chain B: N.258, Y.259, I.261, S.262, N.263, E.266 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:N.258, B:I.261, B:E.266 MG.11: 6 residues within 4Å: Chain B: A.81, E.82, A.84, I.87, H.107, N.112 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:A.81, B:E.82, B:A.84, B:H.107, H2O.11 MG.12: 5 residues within 4Å: Chain A: S.37 Chain B: Y.259, S.260, I.261 Ligands: NAD.1 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:Y.259, B:S.260, B:I.261, H2O.11 MG.13: 5 residues within 4Å: Chain A: E.237, E.241 Chain B: D.201 Ligands: HIO.2, MG.15 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.201, H2O.1, H2O.1, H2O.6 MG.14: 6 residues within 4Å: Chain B: G.36, S.37, Q.38, G.39, L.90 Ligands: NAD.8 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:L.90 MG.15: 4 residues within 4Å: Chain B: D.201, E.205 Ligands: HIO.2, MG.13 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.201, B:E.205, H2O.6, H2O.10

1 x HIS: HISTIDINE(Non-covalent)

HIS.9: 4 residues within 4Å: Chain B: E.341, D.342, L.343, E.344 2 PLIP interactions: 1 Ligand-Ligand interactions, 1 interactions with chain B Hydrogen bonds: H.9, B:E.341

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brinkmann-Chen, S. et al., General approach to reversing ketol-acid reductoisomerase cofactor dependence from NADPH to NADH. Proc.Natl.Acad.Sci.USA (2013)

Release Date

2013-06-26

Peptides

Ketol-acid reductoisomerase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ketol-acid reductoisomerase