SMTL ID : 4xdz.1

Holo structure of ketol-acid reductoisomerase from Ignisphaera aggregans

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.15 Å

Oligo State

homo-dimer

Ligands

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

NDP.1: 25 residues within 4Å: Chain A: G.24, Y.25, G.26, S.27, Q.28, L.47, E.48, R.49, S.53, L.80, V.81, P.82, D.83, V.85, Q.86, A.107, H.108, P.130, S.132, P.133, G.134 Chain B: A.250, V.251, S.252 Ligands: 40E.4 25 PLIP interactions: 23 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Y.25, A:S.27, A:S.27, A:Q.28, A:Q.28, A:D.52, A:S.53, A:S.53, A:S.53, A:D.83, A:Q.86, A:G.134, B:A.250 Water bridges: A:G.26, A:G.26, A:S.27, A:E.48, A:R.49, A:W.54, A:F.79, A:H.108, B:V.251 Salt bridges: A:R.49 pi-Cation interactions: A:R.49, A:R.49 NDP.9: 25 residues within 4Å: Chain A: A.250, V.251, S.252 Chain B: G.24, Y.25, G.26, S.27, Q.28, L.47, E.48, R.49, S.53, L.80, V.81, P.82, D.83, V.85, Q.86, A.107, H.108, P.130, S.132, P.133, G.134 Ligands: 40E.12 29 PLIP interactions: 25 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:Q.28 Hydrogen bonds: B:Y.25, B:S.27, B:S.27, B:Q.28, B:Q.28, B:D.52, B:S.53, B:S.53, B:D.83, B:Q.86, B:G.134, A:A.250 Water bridges: B:G.26, B:G.29, B:E.48, B:R.49, B:D.52, B:W.54, B:F.79, B:H.108, B:F.110, B:Y.295, A:A.250, A:V.251, A:S.252 Salt bridges: B:R.49 pi-Cation interactions: B:R.49, B:R.49

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.191, E.195 Ligands: MG.3, 40E.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.191, A:E.195, H2O.4, H2O.4 MG.3: 5 residues within 4Å: Chain A: K.131, D.191 Chain B: E.231 Ligands: MG.2, 40E.4 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.191, H2O.4, H2O.15, H2O.18, H2O.21 MG.10: 5 residues within 4Å: Chain A: E.231 Chain B: K.131, D.191 Ligands: MG.11, 40E.12 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.191, H2O.4, H2O.7, H2O.10, H2O.16 MG.11: 4 residues within 4Å: Chain B: D.191, E.195 Ligands: MG.10, 40E.12 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.191, B:E.195, H2O.15, H2O.16

2 x 40E: oxo(propan-2-ylamino)acetic acid(Non-covalent)

40E.4: 13 residues within 4Å: Chain A: P.133, D.191, E.195, L.199, V.200 Chain B: E.231, I.235, V.251, S.252, A.255 Ligands: NDP.1, MG.2, MG.3 10 PLIP interactions: 5 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:I.235, B:V.251, A:P.133, A:L.199, A:V.200 Hydrogen bonds: B:E.231, B:S.252 Water bridges: B:S.252, A:K.131, A:K.131 40E.12: 13 residues within 4Å: Chain A: E.231, I.235, V.251, S.252, A.255 Chain B: P.133, D.191, E.195, L.199, V.200 Ligands: NDP.9, MG.10, MG.11 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:I.235, A:V.251, B:P.133, B:L.199, B:V.200 Hydrogen bonds: A:E.231, A:S.252, B:D.191 Water bridges: A:S.252, B:K.131

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.5: 3 residues within 4Å: Chain A: Y.66, K.68, D.69 5 PLIP interactions: 5 interactions with chain A Water bridges: A:S.93, A:S.93 Salt bridges: A:K.68, A:D.69, A:D.69 EPE.13: 3 residues within 4Å: Chain B: Y.66, K.68, D.69 5 PLIP interactions: 5 interactions with chain B Water bridges: B:S.93, B:S.93 Salt bridges: B:K.68, B:D.69, B:D.69

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain A: D.7, L.12, S.39, K.170, R.176 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.7, A:R.176, A:R.176 Water bridges: A:D.7, A:S.39, A:R.176 GOL.7: 5 residues within 4Å: Chain A: M.84, K.87, I.116, Y.295, E.296 5 PLIP interactions: 5 interactions with chain A Water bridges: A:D.83, A:M.84, A:K.87, A:K.87, A:K.87 GOL.8: 4 residues within 4Å: Chain A: F.114, G.285, R.289, I.292 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.289 GOL.14: 5 residues within 4Å: Chain B: D.7, L.12, S.39, K.170, R.176 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.7, B:R.176, B:R.176 Water bridges: B:Y.141, B:R.176 GOL.15: 4 residues within 4Å: Chain B: M.84, I.116, Y.295, E.296 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.296 Water bridges: B:M.84, B:K.87, B:N.111

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

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