SMTL ID : 6l2i.1

IlvC, a ketol-acid reductoisomerase, from Streptococcus pneumoniae_WT

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

homo-dimer

Ligands

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain A: T.268, E.269 Chain B: A.209, E.212 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:E.269 Water bridges: A:I.267, A:E.269, B:A.205, B:E.212, B:E.212 GOL.2: 10 residues within 4Å: Chain A: D.83, E.84, I.85, Q.86, Q.87, F.110, N.111, F.116, V.292, K.296 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.83, A:E.84, A:Q.87, A:N.111, A:K.296 Water bridges: A:E.88 GOL.3: 5 residues within 4Å: Chain A: A.310, E.315, K.316, A.319 Chain B: K.245 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.310 GOL.13: 5 residues within 4Å: Chain B: E.8, S.40, Y.141, K.170, R.176 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.40, B:R.176, B:R.176 Water bridges: B:G.173 GOL.14: 4 residues within 4Å: Chain A: A.209, E.212 Chain B: T.268, E.269 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:E.269 Water bridges: B:E.269, A:A.205, A:A.209, A:E.212, A:E.212 GOL.15: 4 residues within 4Å: Chain A: A.205, E.208, L.312 Chain B: R.248 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.248, B:R.248 Water bridges: A:T.204, A:A.309 GOL.16: 4 residues within 4Å: Chain A: R.248 Chain B: A.205, E.208, L.312 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.248, A:R.248 Water bridges: B:T.204 GOL.17: 6 residues within 4Å: Chain B: K.72, L.73, A.74, D.75, E.99, N.102 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.72, B:D.75, B:N.102, B:N.102 Water bridges: B:K.20, B:E.99

10 x SO4: SULFATE ION(Non-functional Binders)

SO4.4: 3 residues within 4Å: Chain A: R.299, R.306 Chain B: N.253 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:N.253 Water bridges: B:N.253, A:Y.295, A:Y.295 Salt bridges: A:R.299, A:R.306 SO4.5: 2 residues within 4Å: Chain A: V.11, K.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.14 Water bridges: A:V.11 SO4.6: 5 residues within 4Å: Chain A: R.49, P.50, G.51, K.52, S.53 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.52, A:S.53 Water bridges: A:F.54 Salt bridges: A:R.49 SO4.7: 7 residues within 4Å: Chain A: E.8, S.40, Y.141, K.170, G.171, G.173, R.176 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Y.141, A:K.170 Water bridges: A:G.173, A:G.173, A:R.176, A:R.176, A:R.176, A:R.176 Salt bridges: A:R.176 SO4.8: 4 residues within 4Å: Chain A: Q.270, N.274 Chain B: T.268, Q.270 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:T.268, A:Q.270, A:N.274, A:N.274 Water bridges: B:E.269, B:Q.270 SO4.9: 4 residues within 4Å: Chain A: T.268, Q.270 Chain B: Q.270, N.274 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.268, B:Q.270, B:N.274 Water bridges: A:E.269, A:Q.270 SO4.18: 3 residues within 4Å: Chain A: N.253 Chain B: R.299, R.306 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Water bridges: B:R.306, B:R.306 Salt bridges: B:R.299, B:R.306 Hydrogen bonds: A:N.253 SO4.19: 2 residues within 4Å: Chain B: R.49, R.299 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.49, B:R.299 SO4.20: 6 residues within 4Å: Chain A: S.250 Chain B: S.28, H.31, P.133, G.134, H.135 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.28, B:H.135 Salt bridges: B:H.135 Water bridges: A:S.250, A:S.250 SO4.21: 9 residues within 4Å: Chain A: E.231, I.235, A.255 Chain B: D.191, E.195, C.200 Ligands: NAP.10, MG.11, MG.12 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.195, B:E.195, A:E.231

1 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.10: 24 residues within 4Å: Chain A: S.250, I.251, S.252 Chain B: G.25, Y.26, G.27, S.28, Q.29, V.48, R.49, K.52, S.53, V.67, L.80, A.81, P.82, D.83, I.85, Q.86, L.89, A.107, H.108, P.133 Ligands: SO4.21 19 PLIP interactions: 16 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Y.26, B:Y.26, B:S.28, B:S.28, B:Q.29, B:R.49, B:S.53, B:S.53, B:S.53, B:D.83, B:Q.86, A:S.250, A:S.252 Water bridges: B:G.27, B:G.30, B:H.108, B:H.108, A:S.252 Salt bridges: B:R.49

2 x MG: MAGNESIUM ION(Non-covalent)

MG.11: 5 residues within 4Å: Chain A: E.227 Chain B: D.191, E.195 Ligands: MG.12, SO4.21 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.191, B:E.195, H2O.1 MG.12: 4 residues within 4Å: Chain B: D.191, E.195 Ligands: MG.11, SO4.21 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.191, B:E.195, H2O.14, H2O.17, H2O.18

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, G.H. et al., Crystal Structure of IlvC, a Ketol-Acid Reductoisomerase, from Streptococcus Pneumoniae. Crystals (2019)

Release Date

2020-08-12

Peptides

Ketol-acid reductoisomerase (NADP(+)): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ketol-acid reductoisomerase (NADP(+))