SMTL ID : 8a5k.2 (2 other biounits)

Structural analysis of 1-deoxy-D-xylulose 5-phosphate synthase from Pseudomonas aeruginosa and Klebsiella pneumoniae reveals conformational changes upon cofactor binding

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.1: 26 residues within 4Å: Chain A: A.87, V.113, H.115, G.156, H.157, S.158, G.186, D.187, G.188, A.189, N.214, N.216, M.218, S.219, I.220, K.286, H.301, P.344, A.345, M.346, I.368, E.370, F.395, R.398, H.431 Ligands: MG.2 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:I.220 Hydrogen bonds: A:G.156, A:S.158, A:G.186, A:G.186, A:G.188, A:A.189, A:N.216, A:N.216 Water bridges: A:D.112, A:Q.116, A:D.187, A:D.187, A:N.214, A:N.214 Salt bridges: A:H.115, A:H.115, A:K.286 pi-Stacking: A:F.395 TPP.4: 26 residues within 4Å: Chain B: A.87, V.113, H.115, G.156, H.157, S.158, G.186, D.187, G.188, A.189, N.214, N.216, M.218, S.219, I.220, K.286, H.301, P.344, A.345, M.346, I.368, E.370, F.395, R.398, H.431 Ligands: MG.5 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:I.220, B:I.368, B:F.395 Hydrogen bonds: B:G.156, B:S.158, B:G.186, B:G.186, B:G.188, B:A.189, B:N.214, B:N.216 Water bridges: B:Q.116, B:D.187, B:N.216, B:E.370 Salt bridges: B:H.115, B:H.115, B:K.286 pi-Stacking: B:H.115, B:F.395

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: D.187, N.216, M.218 Ligands: TPP.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.187, A:M.218, H2O.2 MG.5: 4 residues within 4Å: Chain B: D.187, N.216, M.218 Ligands: TPP.4 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.187, B:M.218, H2O.11

1 x CA: CALCIUM ION(Non-covalent)

CA.3: 2 residues within 4Å: Chain A: G.299, A.302 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.299, A:A.302, H2O.5, H2O.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hamid, R. et al., 1-deoxy-D-xylulose-5-phosphate synthase from Pseudomonas aeruginosa and Klebsiella pneumoniae reveals conformational changes upon cofactor binding. J.Biol.Chem. (2023)

Release Date

2023-07-05

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
E

1-deoxy-D-xylulose-5-phosphate synthase

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