SMTL ID : 8a45.3 (2 other biounits)

Structural analysis of 1-deoxy-D-xylulose 5-phosphate synthase from Pseudomonas aeruginosa with 2-acetyl thiamine diphosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-12-mer

Ligands

12 x HTL: 2-ACETYL-THIAMINE DIPHOSPHATE(Non-covalent)

HTL.1: 27 residues within 4Å: Chain A: H.84, 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 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:I.368 Hydrogen bonds: A:G.156, A:S.158, A:G.186, A:G.188, A:A.189, A:N.214, A:N.216, A:S.219, A:H.431 Water bridges: A:Q.116, A:D.187, A:N.216, A:E.370 Salt bridges: A:H.115, A:H.115, A:K.286 pi-Stacking: A:F.395 HTL.7: 27 residues within 4Å: Chain B: H.84, 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.8 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:I.368 Hydrogen bonds: B:G.156, B:S.158, B:G.186, B:G.188, B:A.189, B:N.214, B:N.216, B:M.218, B:H.431 Water bridges: B:Q.116, B:D.187, B:D.187, B:E.370 Salt bridges: B:H.115, B:H.115, B:K.286 pi-Stacking: B:F.395 HTL.10: 27 residues within 4Å: Chain C: H.84, 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.11 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:I.368, C:F.395 Hydrogen bonds: C:G.156, C:S.158, C:G.186, C:G.188, C:A.189, C:N.214, C:N.216, C:M.218 Water bridges: C:Q.116, C:D.187, C:N.216, C:E.370 Salt bridges: C:H.115, C:H.115, C:K.286 pi-Stacking: C:F.395 HTL.13: 28 residues within 4Å: Chain D: H.84, A.87, V.113, H.115, F.142, 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.14 20 PLIP interactions: 20 interactions with chain D Hydrophobic interactions: D:I.220, D:I.368, D:I.368 Hydrogen bonds: D:G.156, D:S.158, D:G.186, D:G.188, D:A.189, D:N.214, D:N.216, D:S.219, D:H.431 Water bridges: D:Q.116, D:D.187, D:D.187 Salt bridges: D:H.115, D:H.115, D:K.286 pi-Stacking: D:H.115, D:F.395 HTL.19: 28 residues within 4Å: Chain E: H.84, A.87, V.113, H.115, F.142, 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.20 20 PLIP interactions: 20 interactions with chain E Hydrophobic interactions: E:V.113, E:I.220, E:I.368, E:I.368 Hydrogen bonds: E:G.156, E:S.158, E:G.186, E:G.188, E:A.189, E:N.214, E:N.216 Water bridges: E:D.112, E:Q.116, E:D.187, E:D.187, E:E.370 Salt bridges: E:H.115, E:H.115, E:K.286 pi-Stacking: E:F.395 HTL.23: 27 residues within 4Å: Chain F: H.84, 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.24 19 PLIP interactions: 19 interactions with chain F Hydrophobic interactions: F:I.368, F:F.395 Hydrogen bonds: F:G.156, F:S.158, F:G.186, F:G.188, F:A.189, F:N.214, F:N.216, F:N.216, F:M.218, F:H.431 Water bridges: F:Q.116, F:D.187, F:D.187 Salt bridges: F:H.115, F:H.115, F:K.286 pi-Stacking: F:F.395 HTL.29: 27 residues within 4Å: Chain G: H.84, 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.30 18 PLIP interactions: 18 interactions with chain G Hydrophobic interactions: G:I.368 Hydrogen bonds: G:G.156, G:S.158, G:G.186, G:G.188, G:A.189, G:N.214, G:N.216, G:S.219, G:H.431 Water bridges: G:D.112, G:Q.116, G:D.187, G:N.216 Salt bridges: G:H.115, G:H.115, G:K.286 pi-Stacking: G:F.395 HTL.35: 27 residues within 4Å: Chain H: H.84, 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.36 18 PLIP interactions: 18 interactions with chain H Hydrophobic interactions: H:I.368 Hydrogen bonds: H:G.156, H:S.158, H:G.186, H:G.188, H:A.189, H:N.214, H:N.216, H:M.218, H:H.431 Water bridges: H:D.112, H:Q.116, H:D.187, H:D.187 Salt bridges: H:H.115, H:H.115, H:K.286 pi-Stacking: H:F.395 HTL.38: 27 residues within 4Å: Chain I: H.84, 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.39 18 PLIP interactions: 18 interactions with chain I Hydrophobic interactions: I:I.368, I:F.395 Hydrogen bonds: I:G.156, I:S.158, I:G.186, I:G.188, I:A.189, I:N.214, I:N.216, I:M.218 Water bridges: I:D.112, I:Q.116, I:D.187, I:N.216 Salt bridges: I:H.115, I:H.115, I:K.286 pi-Stacking: I:F.395 HTL.41: 28 residues within 4Å: Chain J: H.84, A.87, V.113, H.115, F.142, 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.42 22 PLIP interactions: 22 interactions with chain J Hydrophobic interactions: J:I.220, J:I.368, J:I.368 Hydrogen bonds: J:G.156, J:S.158, J:G.186, J:G.188, J:A.189, J:N.214, J:N.216, J:S.219, J:H.431 Water bridges: J:D.112, J:Q.116, J:D.187, J:D.187, J:E.370 Salt bridges: J:H.115, J:H.115, J:K.286 pi-Stacking: J:H.115, J:F.395 HTL.47: 28 residues within 4Å: Chain K: H.84, A.87, V.113, H.115, F.142, 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.48 18 PLIP interactions: 18 interactions with chain K Hydrophobic interactions: K:V.113, K:I.220, K:I.368, K:I.368 Hydrogen bonds: K:G.156, K:S.158, K:G.186, K:G.188, K:A.189, K:N.214, K:N.216 Water bridges: K:Q.116, K:D.187, K:D.187 Salt bridges: K:H.115, K:H.115, K:K.286 pi-Stacking: K:F.395 HTL.51: 27 residues within 4Å: Chain L: H.84, 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.52 21 PLIP interactions: 21 interactions with chain L Hydrophobic interactions: L:I.368, L:F.395 Hydrogen bonds: L:G.156, L:S.158, L:G.186, L:G.188, L:A.189, L:N.214, L:N.216, L:N.216, L:M.218, L:H.431 Water bridges: L:D.112, L:Q.116, L:D.187, L:D.187, L:E.370 Salt bridges: L:H.115, L:H.115, L:K.286 pi-Stacking: L:F.395

12 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: D.187, G.188, N.216, M.218, S.219 Ligands: HTL.1 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.187, A:M.218, H2O.4 MG.8: 6 residues within 4Å: Chain B: D.187, G.188, N.216, M.218, S.219 Ligands: HTL.7 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.187, B:M.218, H2O.19 MG.11: 6 residues within 4Å: Chain C: D.187, G.188, N.216, M.218, S.219 Ligands: HTL.10 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.187, C:M.218, H2O.34 MG.14: 6 residues within 4Å: Chain D: D.187, G.188, N.216, M.218, S.219 Ligands: HTL.13 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.187, D:M.218, H2O.47 MG.20: 6 residues within 4Å: Chain E: D.187, G.188, N.216, M.218, S.219 Ligands: HTL.19 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.187, E:M.218, H2O.61 MG.24: 6 residues within 4Å: Chain F: D.187, G.188, N.216, M.218, S.219 Ligands: HTL.23 3 PLIP interactions: 2 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.187, F:M.218, H2O.73 MG.30: 6 residues within 4Å: Chain G: D.187, G.188, N.216, M.218, S.219 Ligands: HTL.29 3 PLIP interactions: 2 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.187, G:M.218, H2O.89 MG.36: 6 residues within 4Å: Chain H: D.187, G.188, N.216, M.218, S.219 Ligands: HTL.35 3 PLIP interactions: 2 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:D.187, H:M.218, H2O.103 MG.39: 6 residues within 4Å: Chain I: D.187, G.188, N.216, M.218, S.219 Ligands: HTL.38 3 PLIP interactions: 2 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:D.187, I:M.218, H2O.118 MG.42: 6 residues within 4Å: Chain J: D.187, G.188, N.216, M.218, S.219 Ligands: HTL.41 3 PLIP interactions: 2 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:D.187, J:M.218, H2O.131 MG.48: 6 residues within 4Å: Chain K: D.187, G.188, N.216, M.218, S.219 Ligands: HTL.47 3 PLIP interactions: 2 interactions with chain K, 1 Ligand-Water interactions Metal complexes: K:D.187, K:M.218, H2O.146 MG.52: 6 residues within 4Å: Chain L: D.187, G.188, N.216, M.218, S.219 Ligands: HTL.51 3 PLIP interactions: 2 interactions with chain L, 1 Ligand-Water interactions Metal complexes: L:D.187, L:M.218, H2O.157

24 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.3: 2 residues within 4Å: Chain A: R.501, D.526 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.526, A:D.526, H2O.2, H2O.13, H2O.13 CA.4: 6 residues within 4Å: Chain A: K.386, D.413, Y.465, F.467, D.468, G.469 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.413, A:Y.465, A:F.467, H2O.8, H2O.9 CA.5: 5 residues within 4Å: Chain A: P.476, V.513, Q.514, E.558, L.601 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.558, H2O.2, H2O.14, H2O.15 CA.15: 3 residues within 4Å: Chain D: G.299, A.302, I.303 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:A.302, H2O.52, H2O.52, H2O.54, H2O.55 CA.16: 2 residues within 4Å: Chain D: D.486, D.488 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.486, D:D.488, H2O.46 CA.17: 5 residues within 4Å: Chain D: D.455, E.456, K.459, R.500, R.533 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.455, D:E.456, H2O.45, H2O.53 CA.18: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.21: 2 residues within 4Å: Chain E: D.486, D.488 5 PLIP interactions: 2 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:D.486, E:D.488, H2O.67, H2O.67, H2O.68 CA.25: 2 residues within 4Å: Chain F: D.486, D.488 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.486, F:D.486, F:D.488, H2O.82 CA.26: 3 residues within 4Å: Chain F: G.299, A.302, I.303 5 PLIP interactions: 2 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:G.299, F:A.302, H2O.80, H2O.81, H2O.82 CA.27: 6 residues within 4Å: Chain F: K.386, D.413, G.464, Y.465, F.467, G.469 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.413, F:G.464, F:Y.465, F:F.467 CA.28: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.31: 3 residues within 4Å: Chain C: D.273 Chain G: R.501, D.526 5 PLIP interactions: 2 interactions with chain G, 3 Ligand-Water interactions Metal complexes: G:D.526, G:D.526, H2O.86, H2O.97, H2O.97 CA.32: 6 residues within 4Å: Chain G: K.386, D.413, Y.465, F.467, D.468, G.469 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:D.413, G:Y.465, G:F.467, H2O.93, H2O.94 CA.33: 5 residues within 4Å: Chain G: P.476, V.513, Q.514, E.558, L.601 4 PLIP interactions: 1 interactions with chain G, 3 Ligand-Water interactions Metal complexes: G:E.558, H2O.86, H2O.98, H2O.99 CA.43: 3 residues within 4Å: Chain J: G.299, A.302, I.303 5 PLIP interactions: 1 interactions with chain J, 4 Ligand-Water interactions Metal complexes: J:A.302, H2O.136, H2O.137, H2O.139, H2O.140 CA.44: 2 residues within 4Å: Chain J: D.486, D.488 3 PLIP interactions: 2 interactions with chain J, 1 Ligand-Water interactions Metal complexes: J:D.486, J:D.488, H2O.130 CA.45: 5 residues within 4Å: Chain J: D.455, E.456, K.459, R.500, R.533 4 PLIP interactions: 2 interactions with chain J, 2 Ligand-Water interactions Metal complexes: J:D.455, J:E.456, H2O.130, H2O.137 CA.46: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.49: 2 residues within 4Å: Chain K: D.486, D.488 5 PLIP interactions: 2 interactions with chain K, 3 Ligand-Water interactions Metal complexes: K:D.486, K:D.488, H2O.151, H2O.151, H2O.152 CA.53: 2 residues within 4Å: Chain L: D.486, D.488 4 PLIP interactions: 3 interactions with chain L, 1 Ligand-Water interactions Metal complexes: L:D.486, L:D.486, L:D.488, H2O.166 CA.54: 3 residues within 4Å: Chain L: G.299, A.302, I.303 5 PLIP interactions: 2 interactions with chain L, 3 Ligand-Water interactions Metal complexes: L:G.299, L:A.302, H2O.164, H2O.166, H2O.166 CA.55: 6 residues within 4Å: Chain L: K.386, D.413, G.464, Y.465, F.467, G.469 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:D.413, L:G.464, L:Y.465, L:F.467 CA.56: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

NA.6: 3 residues within 4Å: Chain A: G.299, A.302, I.303 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.299 NA.9: 3 residues within 4Å: Chain B: G.299, A.302, I.303 2 PLIP interactions: 2 interactions with chain B Water bridges: B:G.299, B:H.301 NA.12: 4 residues within 4Å: Chain C: G.299, Y.300, A.302, I.303 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.299 NA.22: 3 residues within 4Å: Chain E: G.299, A.302, I.303 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:A.302 NA.34: 3 residues within 4Å: Chain G: G.299, A.302, I.303 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:G.299 NA.37: 3 residues within 4Å: Chain H: G.299, A.302, I.303 2 PLIP interactions: 2 interactions with chain H Water bridges: H:G.299, H:H.301 NA.40: 4 residues within 4Å: Chain I: G.299, Y.300, A.302, I.303 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:A.302 NA.50: 3 residues within 4Å: Chain K: G.299, A.302, I.303 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:A.302

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: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
A

H
B

I
C

J
D

K
E

L
F

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

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