SMTL ID : 8qoc.2 (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: 5 residues within 4Å: Chain A: H.112, R.134, R.135 Chain B: T.181, 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.3 Ligand excluded by PLIP PO4.4: 5 residues within 4Å: Chain A: T.181, K.184 Chain B: H.112, R.134, R.135 Ligand excluded by PLIP PO4.5: 9 residues within 4Å: Chain B: P.46, P.149, G.150, G.210, G.211, V.231, G.232, S.233 Ligands: CL.6 Ligand excluded by PLIP PO4.7: 5 residues within 4Å: Chain C: H.112, E.131, R.134, R.135 Chain L: K.184 Ligand excluded by PLIP PO4.8: 9 residues within 4Å: Chain C: P.46, P.149, G.150, G.210, G.211, V.231, G.232, S.233 Ligands: MG.9 Ligand excluded by PLIP PO4.10: 4 residues within 4Å: Chain D: H.112, R.134, R.135 Chain G: K.184 Ligand excluded by PLIP PO4.11: 9 residues within 4Å: Chain D: 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: 5 residues within 4Å: Chain E: H.112, R.134, R.135 Chain F: T.181, K.184 Ligand excluded by PLIP PO4.14: 9 residues within 4Å: Chain E: P.46, P.149, G.150, G.210, G.211, V.231, G.232, S.233 Ligands: CL.15 Ligand excluded by PLIP PO4.16: 5 residues within 4Å: Chain E: T.181, K.184 Chain F: H.112, R.134, R.135 Ligand excluded by PLIP PO4.17: 9 residues within 4Å: Chain F: P.46, P.149, G.150, G.210, G.211, V.231, G.232, S.233 Ligands: CL.18 Ligand excluded by PLIP PO4.19: 5 residues within 4Å: Chain D: K.184 Chain G: H.112, E.131, R.134, R.135 Ligand excluded by PLIP PO4.20: 9 residues within 4Å: Chain G: P.46, P.149, G.150, G.210, G.211, V.231, G.232, S.233 Ligands: MG.21 Ligand excluded by PLIP PO4.22: 4 residues within 4Å: Chain H: H.112, R.134, R.135 Chain K: K.184 Ligand excluded by PLIP PO4.23: 9 residues within 4Å: Chain H: P.46, P.149, G.150, G.210, G.211, V.231, G.232, S.233 Ligands: CL.24 Ligand excluded by PLIP PO4.25: 5 residues within 4Å: Chain I: H.112, R.134, R.135 Chain J: T.181, K.184 Ligand excluded by PLIP PO4.26: 9 residues within 4Å: Chain I: P.46, P.149, G.150, G.210, G.211, V.231, G.232, S.233 Ligands: CL.27 Ligand excluded by PLIP PO4.28: 5 residues within 4Å: Chain I: T.181, K.184 Chain J: H.112, R.134, R.135 Ligand excluded by PLIP PO4.29: 9 residues within 4Å: Chain J: P.46, P.149, G.150, G.210, G.211, V.231, G.232, S.233 Ligands: CL.30 Ligand excluded by PLIP PO4.31: 5 residues within 4Å: Chain H: K.184 Chain K: H.112, E.131, R.134, R.135 Ligand excluded by PLIP PO4.32: 9 residues within 4Å: Chain K: P.46, P.149, G.150, G.210, G.211, V.231, G.232, S.233 Ligands: MG.33 Ligand excluded by PLIP PO4.34: 4 residues within 4Å: Chain C: K.184 Chain L: H.112, R.134, R.135 Ligand excluded by PLIP PO4.35: 9 residues within 4Å: Chain L: P.46, P.149, G.150, G.210, G.211, V.231, G.232, S.233 Ligands: CL.36 Ligand excluded by PLIP

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

CL.3: 3 residues within 4Å: Chain A: D.21, K.78 Ligands: PO4.2 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain B: D.21, K.78 Ligands: PO4.5 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain D: D.21, K.78 Ligands: PO4.11 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain E: D.21, K.78 Ligands: PO4.14 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain F: D.21, K.78 Ligands: PO4.17 Ligand excluded by PLIP CL.24: 3 residues within 4Å: Chain H: D.21, K.78 Ligands: PO4.23 Ligand excluded by PLIP CL.27: 3 residues within 4Å: Chain I: D.21, K.78 Ligands: PO4.26 Ligand excluded by PLIP CL.30: 3 residues within 4Å: Chain J: D.21, K.78 Ligands: PO4.29 Ligand excluded by PLIP CL.36: 3 residues within 4Å: Chain L: D.21, K.78 Ligands: PO4.35 Ligand excluded by PLIP

3 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 3 residues within 4Å: Chain C: D.21, K.78 Ligands: PO4.8 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:D.21 MG.21: 3 residues within 4Å: Chain G: D.21, K.78 Ligands: PO4.20 1 PLIP interactions: 1 interactions with chain G Metal complexes: G:D.21 MG.33: 3 residues within 4Å: Chain K: D.21, K.78 Ligands: PO4.32 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:D.21

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
C

B
F

C
G

D
H

E
C

F
F

G
G

H
H

I
C

J
F

K
G

L
H

Pyridoxal 5'-phosphate synthase subunit PdxS

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