SMTL ID : 8a29.1 (2 other biounits)

Apo 1-deoxy-D-xylulose 5-phosphate synthase from Pseudomonas aeruginosa

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 3 residues within 4Å: Chain A: N.200, L.248 Chain B: T.191 No protein-ligand interaction detected (PLIP) GOL.8: 4 residues within 4Å: Chain B: N.200, S.203, E.204, L.248 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.200 GOL.9: 9 residues within 4Å: Chain A: M.562 Chain B: V.535, K.536, P.537, L.538, E.540, A.568, E.571, F.572 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.538 Water bridges: B:V.535, B:E.571

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: G.186, D.187, G.188, N.216 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.187, H2O.1, H2O.2 MG.3: 8 residues within 4Å: Chain A: K.386, D.413, G.464, Y.465, L.466, F.467, D.468, G.469 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.413, A:D.413, A:Y.465, A:F.467, H2O.7 MG.10: 5 residues within 4Å: Chain B: G.186, D.187, G.188, N.216, D.217 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.187, B:D.217, H2O.14 MG.11: 6 residues within 4Å: Chain B: S.452, D.453, P.481, H.483, L.515, A.516 No protein-ligand interaction detected (PLIP)

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 2 residues within 4Å: Chain A: E.571 Chain B: M.562 Ligand excluded by PLIP

2 x NA: SODIUM ION(Non-functional Binders)

NA.5: 3 residues within 4Å: Chain A: G.299, A.302, I.303 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.302 Water bridges: A:A.302 NA.12: 2 residues within 4Å: Chain B: D.486, D.488 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.486

4 x CA: CALCIUM ION(Non-covalent)

CA.6: 4 residues within 4Å: Chain A: R.108, R.145, T.152 Chain B: C.382 No protein-ligand interaction detected (PLIP) CA.7: 2 residues within 4Å: Chain A: Q.327, R.358 No protein-ligand interaction detected (PLIP) CA.13: 3 residues within 4Å: Chain B: K.347, Y.363, D.365 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:Y.363, B:D.365, H2O.24, H2O.26 CA.14: 5 residues within 4Å: Chain B: D.455, E.456, K.459, R.500, R.533 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.455, B:E.456, H2O.15, H2O.23

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

2023-06-14

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
E

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

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