SMTL ID : 7s04.1

1-deoxy-D-xylulose 5-phosphate reductoisomerase (IspC) from Acinetobacter baumannii in complex with FR900098, NADPH, and a magnesium ion

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.52 Å

Oligo State

homo-dimer

Ligands

2 x F98: 3-[ethanoyl(hydroxy)amino]propylphosphonic acid(Non-covalent)

F98.1: 17 residues within 4Å: Chain A: K.134, D.159, S.160, E.161, A.193, S.194, H.217, W.220, M.222, I.226, S.230, N.235, K.236, E.239, M.284 Ligands: MG.2, NDP.3 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.220 Hydrogen bonds: A:K.134, A:S.160, A:S.194, A:S.194, A:N.235, A:N.235, A:K.236, A:K.236 Water bridges: A:G.195, A:G.196, A:K.236 F98.4: 17 residues within 4Å: Chain B: K.134, D.159, S.160, E.161, A.193, S.194, H.217, W.220, M.222, I.226, S.230, N.235, K.236, E.239, M.284 Ligands: MG.5, NDP.6 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:W.220 Hydrogen bonds: B:K.134, B:S.160, B:S.194, B:S.194, B:N.235, B:N.235, B:K.236, B:K.236 Water bridges: B:G.195, B:G.196, B:K.236

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: K.134, D.159, S.160, E.161, E.239 Ligands: F98.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.159, A:E.161, A:E.239 MG.5: 6 residues within 4Å: Chain B: K.134, D.159, S.160, E.161, E.239 Ligands: F98.4 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.159, B:E.161, B:E.239

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

NDP.3: 25 residues within 4Å: Chain A: G.17, V.18, T.19, G.20, S.21, I.22, A.44, H.45, S.46, R.47, A.109, I.110, V.111, G.112, A.114, A.132, N.133, K.134, E.135, D.159, M.222, G.223, I.226, M.284 Ligands: F98.1 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:I.22, A:I.226 Hydrogen bonds: A:G.17, A:T.19, A:T.19, A:T.19, A:G.20, A:S.21, A:S.21, A:S.21, A:I.22, A:H.45, A:S.46, A:R.47, A:R.47, A:I.110, A:V.111, A:G.112, A:N.133, A:K.134, A:E.135, A:G.223 Water bridges: A:G.23, A:Q.91, A:Q.224, A:Q.224, A:Q.224 Salt bridges: A:R.47 pi-Stacking: A:H.45 NDP.6: 25 residues within 4Å: Chain B: G.17, V.18, T.19, G.20, S.21, I.22, A.44, H.45, S.46, R.47, A.109, I.110, V.111, G.112, A.114, A.132, N.133, K.134, E.135, D.159, M.222, G.223, I.226, M.284 Ligands: F98.4 32 PLIP interactions: 32 interactions with chain B Hydrophobic interactions: B:I.22, B:I.226 Hydrogen bonds: B:G.17, B:T.19, B:T.19, B:T.19, B:G.20, B:S.21, B:S.21, B:S.21, B:I.22, B:H.45, B:S.46, B:R.47, B:R.47, B:I.110, B:V.111, B:G.112, B:N.133, B:K.134, B:E.135, B:G.223 Water bridges: B:G.23, B:S.46, B:S.46, B:R.47, B:Q.91, B:Q.224, B:Q.224, B:Q.224 Salt bridges: B:R.47 pi-Stacking: B:H.45

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ball, H.S. et al., Characterization and Inhibition of 1-Deoxy-d-Xylulose 5-Phosphate Reductoisomerase: A Promising Drug Target in Acinetobacter baumannii and Klebsiella pneumoniae . Acs Infect Dis. (2021)

Release Date

2021-11-03

Peptides

1-deoxy-D-xylulose 5-phosphate reductoisomerase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

1-deoxy-D-xylulose 5-phosphate reductoisomerase

Related Entries With Identical Sequence