SMTL ID : 7toc.1

Crystal Structure of the Mitochondrial Ketol-acid Reductoisomerase IlvC from Candida auris

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.43 Å

Oligo State

homo-dimer

Ligands

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

NDP.1: 32 residues within 4Å: Chain A: G.52, Y.53, G.54, S.55, Q.56, G.57, V.75, R.76, A.80, S.81, L.112, L.113, S.114, D.115, A.117, Q.118, E.120, T.121, S.138, H.139, P.164, G.166, S.167, G.168, Y.332, R.333 Chain B: C.284, S.285, T.286, R.289 Ligands: MLI.2, MG.5 28 PLIP interactions: 26 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Y.53, A:G.54, A:S.55, A:S.55, A:Q.56, A:Q.56, A:G.57, A:A.80, A:S.81, A:S.81, A:S.81, A:L.113, A:S.114, A:S.114, A:D.115, A:Q.118, A:E.120, A:H.139, A:G.166, A:G.168, B:T.286, B:R.289 Water bridges: A:R.76, A:W.82, A:H.139 Salt bridges: A:R.76, A:R.333 pi-Cation interactions: A:R.76 NDP.6: 31 residues within 4Å: Chain A: C.284, S.285, T.286, R.289 Chain B: G.52, Y.53, G.54, S.55, Q.56, G.57, V.75, R.76, A.80, S.81, L.112, L.113, S.114, D.115, A.117, Q.118, E.120, T.121, S.138, H.139, P.164, G.166, S.167, G.168, Y.332, R.333 Ligands: MLI.4 28 PLIP interactions: 25 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:Q.56 Hydrogen bonds: B:Y.53, B:G.54, B:S.55, B:Q.56, B:Q.56, B:G.57, B:A.80, B:S.81, B:S.81, B:S.81, B:L.113, B:S.114, B:S.114, B:D.115, B:Q.118, B:E.120, B:E.120, B:G.166, B:G.168, B:Y.332, A:T.286, A:R.289 Water bridges: B:R.76, A:S.285 Salt bridges: B:R.76, B:R.333 pi-Cation interactions: B:R.76

2 x MLI: MALONATE ION(Non-functional Binders)

MLI.2: 11 residues within 4Å: Chain A: P.164, D.223, E.227 Chain B: E.259, E.263, C.284, S.285, A.288 Ligands: NDP.1, MG.5, MG.10 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.285, B:S.285, A:P.164 Salt bridges: A:K.165 MLI.4: 9 residues within 4Å: Chain A: E.263, C.284, S.285, A.288 Chain B: D.223, E.227 Ligands: NDP.6, MG.8, MG.9 11 PLIP interactions: 4 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:A.288 Hydrogen bonds: A:E.263, A:S.285 Water bridges: A:S.285, B:K.165, B:K.165, B:K.165, B:K.165, B:E.227, B:E.227 Salt bridges: B:K.165

2 x ACY: ACETIC ACID(Non-functional Binders)

ACY.3: 2 residues within 4Å: Chain A: R.169 Chain B: Y.279 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Water bridges: A:Y.58, A:S.173 Salt bridges: A:R.169, B:K.274 Hydrogen bonds: B:Y.279 ACY.7: 5 residues within 4Å: Chain A: K.274, Y.275, Y.279 Chain B: R.169, S.173 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Salt bridges: A:K.274, B:R.169 Hydrophobic interactions: B:R.169 Water bridges: B:R.169

4 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 6 residues within 4Å: Chain A: H.139, D.223, E.227 Chain B: S.285 Ligands: NDP.1, MLI.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.223, A:E.227, A:E.227, H2O.1 MG.8: 4 residues within 4Å: Chain B: H.139, D.223, E.227 Ligands: MLI.4 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.223, B:E.227, H2O.1, H2O.2 MG.9: 5 residues within 4Å: Chain A: E.259, E.263 Chain B: K.165, D.223 Ligands: MLI.4 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.223, H2O.1, H2O.2 MG.10: 5 residues within 4Å: Chain A: K.165, D.223 Chain B: E.259, E.263 Ligands: MLI.2 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Metal complexes: A:D.223, B:E.259, B:E.263

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y. et al., Crystal Structure of the Mitochondrial Ketol-acid Reductoisomerase IlvC from Candida auris. To Be Published

Release Date

2022-02-16

Peptides

Ketol-acid reductoisomerase, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ketol-acid reductoisomerase, mitochondrial