SMTL ID : 4xdy.1

Structure of NADH-preferring ketol-acid reductoisomerase from an uncultured archean

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.53 Å

Oligo State

homo-dimer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.195, E.199 Ligands: MG.2, HIO.6 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.195, A:E.199, H2O.2, H2O.6 MG.2: 5 residues within 4Å: Chain A: D.195, E.199 Chain B: E.235 Ligands: MG.1, HIO.6 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.195, H2O.2, H2O.8, H2O.8 MG.4: 2 residues within 4Å: Chain A: N.257, E.260 No protein-ligand interaction detected (PLIP) MG.8: 4 residues within 4Å: Chain B: D.195, E.199 Ligands: HIO.7, MG.9 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.195, B:E.199, H2O.8, H2O.8 MG.9: 5 residues within 4Å: Chain A: E.235 Chain B: K.135, D.195 Ligands: HIO.7, MG.8 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.195, H2O.1, H2O.1, H2O.8 MG.11: 1 residues within 4Å: Chain B: N.257 No protein-ligand interaction detected (PLIP)

2 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.3: 26 residues within 4Å: Chain A: G.23, Y.24, G.25, A.26, Q.27, E.46, L.50, N.55, S.57, L.84, L.85, P.86, D.87, V.89, Q.90, I.93, S.111, H.112, P.134, A.136, P.137, G.138 Chain B: V.254, I.255, S.256 Ligands: HIO.6 19 PLIP interactions: 14 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:Q.27 Hydrogen bonds: A:A.26, A:Q.27, A:N.55, A:S.57, A:S.57, A:L.85, A:D.87, A:Q.90, A:A.136, A:G.138, B:S.256 Water bridges: A:G.25, A:G.28, A:H.112, B:V.254, B:I.255, B:N.257, B:N.257 NAI.10: 26 residues within 4Å: Chain A: V.254, I.255, S.256 Chain B: G.23, Y.24, G.25, A.26, Q.27, E.46, L.50, N.55, S.57, L.84, L.85, P.86, D.87, V.89, Q.90, I.93, S.111, H.112, P.134, A.136, P.137, G.138 Ligands: HIO.7 20 PLIP interactions: 16 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:Q.27 Hydrogen bonds: B:A.26, B:Q.27, B:Q.27, B:N.55, B:S.57, B:S.57, B:L.85, B:D.87, B:Q.90, B:A.136, B:G.138, A:S.256 Water bridges: B:G.25, B:G.28, B:H.112, B:Y.299, A:N.257, A:N.257, A:N.257

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: D.29, N.33, K.60, D.64, R.142 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.29, A:K.60, A:D.64, A:R.142 Water bridges: A:N.33, A:N.33 GOL.12: 5 residues within 4Å: Chain B: D.29, N.33, K.60, D.64, R.142 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:D.29, B:K.60, B:D.64, B:R.142 Water bridges: B:N.33, B:N.33, B:D.37

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

HIO.6: 14 residues within 4Å: Chain A: A.136, P.137, D.195, E.199, L.203, C.204 Chain B: E.235, I.239, I.255, S.256, A.259 Ligands: MG.1, MG.2, NAI.3 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:I.255, A:P.137, A:L.203 Hydrogen bonds: B:S.256 Water bridges: B:S.256, B:S.256, A:H.112 HIO.7: 14 residues within 4Å: Chain A: E.235, I.239, I.255, S.256, A.259 Chain B: A.136, P.137, D.195, E.199, L.203, C.204 Ligands: MG.8, MG.9, NAI.10 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:P.137, B:L.203 Water bridges: B:K.135, B:K.135, B:K.135, B:K.135, B:K.135, A:S.256 Hydrogen bonds: A:S.256

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cahn, J.K. et al., Cofactor specificity motifs and the induced fit mechanism in class I ketol-acid reductoisomerases. Biochem.J. (2015)

Release Date

2015-04-22

Peptides

Ketol-acid reductoisomerase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ketol-acid reductoisomerase