SMTL ID : 8qoc.1 (1 other biounit)

Crystal structure of Staphylococcus aureus PLP Synthase (Pdx1)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.83 Å

Oligo State

homo-12-mer

Ligands

24 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 4 residues within 4Å: Chain A: H.112, R.134, R.135 Chain B: K.184 Ligand excluded by PLIP PO4.2: 9 residues within 4Å: Chain A: P.46, P.149, G.150, G.210, G.211, V.231, G.232, S.233 Ligands: CL.4 Ligand excluded by PLIP PO4.6: 5 residues within 4Å: Chain A: T.181, K.184 Chain B: H.112, R.134, R.135 Ligand excluded by PLIP PO4.7: 8 residues within 4Å: Chain B: P.46, P.149, G.150, G.210, G.211, G.232, S.233 Ligands: CL.9 Ligand excluded by PLIP PO4.10: 5 residues within 4Å: Chain C: H.112, R.134, R.135 Chain D: T.181, K.184 Ligand excluded by PLIP PO4.11: 9 residues within 4Å: Chain C: P.46, P.149, G.150, G.210, G.211, V.231, G.232, S.233 Ligands: CL.12 Ligand excluded by PLIP PO4.13: 4 residues within 4Å: Chain C: K.184 Chain D: H.112, R.134, R.135 Ligand excluded by PLIP PO4.14: 9 residues within 4Å: Chain D: D.21, P.46, P.149, G.150, G.210, G.211, G.232, S.233, G.234 Ligand excluded by PLIP PO4.18: 4 residues within 4Å: Chain E: H.112, R.134, R.135 Chain F: K.184 Ligand excluded by PLIP PO4.19: 9 residues within 4Å: Chain E: P.46, P.149, G.150, G.210, G.211, V.231, G.232, S.233 Ligands: CL.21 Ligand excluded by PLIP PO4.23: 5 residues within 4Å: Chain E: T.181, K.184 Chain F: H.112, R.134, R.135 Ligand excluded by PLIP PO4.24: 8 residues within 4Å: Chain F: P.46, P.149, G.150, G.210, G.211, G.232, S.233 Ligands: CL.26 Ligand excluded by PLIP PO4.27: 5 residues within 4Å: Chain G: H.112, R.134, R.135 Chain H: T.181, K.184 Ligand excluded by PLIP PO4.28: 9 residues within 4Å: Chain G: P.46, P.149, G.150, G.210, G.211, V.231, G.232, S.233 Ligands: CL.29 Ligand excluded by PLIP PO4.30: 4 residues within 4Å: Chain G: K.184 Chain H: H.112, R.134, R.135 Ligand excluded by PLIP PO4.31: 9 residues within 4Å: Chain H: D.21, P.46, P.149, G.150, G.210, G.211, G.232, S.233, G.234 Ligand excluded by PLIP PO4.35: 4 residues within 4Å: Chain I: H.112, R.134, R.135 Chain J: K.184 Ligand excluded by PLIP PO4.36: 9 residues within 4Å: Chain I: P.46, P.149, G.150, G.210, G.211, V.231, G.232, S.233 Ligands: CL.38 Ligand excluded by PLIP PO4.40: 5 residues within 4Å: Chain I: T.181, K.184 Chain J: H.112, R.134, R.135 Ligand excluded by PLIP PO4.41: 8 residues within 4Å: Chain J: P.46, P.149, G.150, G.210, G.211, G.232, S.233 Ligands: CL.43 Ligand excluded by PLIP PO4.44: 5 residues within 4Å: Chain K: H.112, R.134, R.135 Chain L: T.181, K.184 Ligand excluded by PLIP PO4.45: 9 residues within 4Å: Chain K: P.46, P.149, G.150, G.210, G.211, V.231, G.232, S.233 Ligands: CL.46 Ligand excluded by PLIP PO4.47: 4 residues within 4Å: Chain K: K.184 Chain L: H.112, R.134, R.135 Ligand excluded by PLIP PO4.48: 9 residues within 4Å: Chain L: D.21, P.46, P.149, G.150, G.210, G.211, G.232, S.233, G.234 Ligand excluded by PLIP

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 5 residues within 4Å: Chain A: T.253, H.254, Y.255, Q.256, D.257 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.254, A:Q.256, A:D.257 EDO.8: 6 residues within 4Å: Chain B: T.214, Q.216, A.265, E.267, L.268, T.270 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.216, B:T.270 EDO.20: 5 residues within 4Å: Chain E: T.253, H.254, Y.255, Q.256, D.257 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:H.254, E:Q.256, E:D.257 EDO.25: 6 residues within 4Å: Chain F: T.214, Q.216, A.265, E.267, L.268, T.270 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:Q.216, F:T.270 EDO.37: 5 residues within 4Å: Chain I: T.253, H.254, Y.255, Q.256, D.257 3 PLIP interactions: 3 interactions with chain I Hydrogen bonds: I:H.254, I:Q.256, I:D.257 EDO.42: 6 residues within 4Å: Chain J: T.214, Q.216, A.265, E.267, L.268, T.270 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:Q.216, J:T.270

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

CL.4: 2 residues within 4Å: Chain A: D.21 Ligands: PO4.2 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain B: D.21, K.78 Ligands: PO4.7 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain C: D.21, K.78 Ligands: PO4.11 Ligand excluded by PLIP CL.15: 2 residues within 4Å: Chain D: D.21, K.78 Ligand excluded by PLIP CL.16: 1 residues within 4Å: Chain D: Q.117 Ligand excluded by PLIP CL.21: 2 residues within 4Å: Chain E: D.21 Ligands: PO4.19 Ligand excluded by PLIP CL.26: 3 residues within 4Å: Chain F: D.21, K.78 Ligands: PO4.24 Ligand excluded by PLIP CL.29: 3 residues within 4Å: Chain G: D.21, K.78 Ligands: PO4.28 Ligand excluded by PLIP CL.32: 2 residues within 4Å: Chain H: D.21, K.78 Ligand excluded by PLIP CL.33: 1 residues within 4Å: Chain H: Q.117 Ligand excluded by PLIP CL.38: 2 residues within 4Å: Chain I: D.21 Ligands: PO4.36 Ligand excluded by PLIP CL.43: 3 residues within 4Å: Chain J: D.21, K.78 Ligands: PO4.41 Ligand excluded by PLIP CL.46: 3 residues within 4Å: Chain K: D.21, K.78 Ligands: PO4.45 Ligand excluded by PLIP CL.49: 2 residues within 4Å: Chain L: D.21, K.78 Ligand excluded by PLIP CL.50: 1 residues within 4Å: Chain L: Q.117 Ligand excluded by PLIP

6 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 2 residues within 4Å: Chain A: Q.216, A.265 No protein-ligand interaction detected (PLIP) MG.17: 1 residues within 4Å: Chain D: E.267 No protein-ligand interaction detected (PLIP) MG.22: 2 residues within 4Å: Chain E: Q.216, A.265 No protein-ligand interaction detected (PLIP) MG.34: 1 residues within 4Å: Chain H: E.267 No protein-ligand interaction detected (PLIP) MG.39: 2 residues within 4Å: Chain I: Q.216, A.265 No protein-ligand interaction detected (PLIP) MG.51: 1 residues within 4Å: Chain L: E.267 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Barra, A.L.C. et al., Structure and dynamics of the staphylococcal pyridoxal 5-phosphate synthase complex reveal transient interactions at the enzyme interface. J.Biol.Chem. (2024)

Release Date

2024-10-02

Peptides

Pyridoxal 5'-phosphate synthase subunit PdxS: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
E

E
A

F
B

G
D

H
E

I
A

J
B

K
D

L
E

Pyridoxal 5'-phosphate synthase subunit PdxS

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