SMTL ID : 8u9e.1

Crystal Structure of Staphylococcus aureus Pdx1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.02 Å

Oligo State

homo-12-mer

Ligands

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

EDO.1: 2 residues within 4Å: Chain A: P.155, G.156 Ligand excluded by PLIP EDO.2: 5 residues within 4Å: Chain A: D.27, K.84, G.216, F.236, G.238 Ligand excluded by PLIP EDO.4: 5 residues within 4Å: Chain B: R.133, N.134, E.137, R.140 Ligands: PO4.10 Ligand excluded by PLIP EDO.5: 2 residues within 4Å: Chain B: F.124, T.125 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain B: D.27, K.84, G.216, F.236, V.237 Ligand excluded by PLIP EDO.11: 2 residues within 4Å: Chain C: P.155, G.156 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain C: D.27, K.84, G.216, F.236, G.238 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain D: R.133, N.134, E.137, R.140 Ligands: PO4.20 Ligand excluded by PLIP EDO.15: 2 residues within 4Å: Chain D: F.124, T.125 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain D: D.27, K.84, G.216, F.236, V.237 Ligand excluded by PLIP EDO.21: 2 residues within 4Å: Chain E: P.155, G.156 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain E: D.27, K.84, G.216, F.236, G.238 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain F: R.133, N.134, E.137, R.140 Ligands: PO4.30 Ligand excluded by PLIP EDO.25: 2 residues within 4Å: Chain F: F.124, T.125 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain F: D.27, K.84, G.216, F.236, V.237 Ligand excluded by PLIP EDO.31: 2 residues within 4Å: Chain G: P.155, G.156 Ligand excluded by PLIP EDO.32: 5 residues within 4Å: Chain G: D.27, K.84, G.216, F.236, G.238 Ligand excluded by PLIP EDO.34: 5 residues within 4Å: Chain H: R.133, N.134, E.137, R.140 Ligands: PO4.40 Ligand excluded by PLIP EDO.35: 2 residues within 4Å: Chain H: F.124, T.125 Ligand excluded by PLIP EDO.38: 5 residues within 4Å: Chain H: D.27, K.84, G.216, F.236, V.237 Ligand excluded by PLIP EDO.41: 2 residues within 4Å: Chain I: P.155, G.156 Ligand excluded by PLIP EDO.42: 5 residues within 4Å: Chain I: D.27, K.84, G.216, F.236, G.238 Ligand excluded by PLIP EDO.44: 5 residues within 4Å: Chain J: R.133, N.134, E.137, R.140 Ligands: PO4.50 Ligand excluded by PLIP EDO.45: 2 residues within 4Å: Chain J: F.124, T.125 Ligand excluded by PLIP EDO.48: 5 residues within 4Å: Chain J: D.27, K.84, G.216, F.236, V.237 Ligand excluded by PLIP EDO.51: 2 residues within 4Å: Chain K: P.155, G.156 Ligand excluded by PLIP EDO.52: 5 residues within 4Å: Chain K: D.27, K.84, G.216, F.236, G.238 Ligand excluded by PLIP EDO.54: 5 residues within 4Å: Chain L: R.133, N.134, E.137, R.140 Ligands: PO4.60 Ligand excluded by PLIP EDO.55: 2 residues within 4Å: Chain L: F.124, T.125 Ligand excluded by PLIP EDO.58: 5 residues within 4Å: Chain L: D.27, K.84, G.216, F.236, V.237 Ligand excluded by PLIP

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

PO4.3: 5 residues within 4Å: Chain A: H.118, E.137, R.140, R.141 Chain K: K.190 Ligand excluded by PLIP PO4.6: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PO4.10: 5 residues within 4Å: Chain B: H.118, E.137, R.140, R.141 Ligands: EDO.4 Ligand excluded by PLIP PO4.13: 5 residues within 4Å: Chain C: H.118, E.137, R.140, R.141 Chain I: K.190 Ligand excluded by PLIP PO4.16: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PO4.20: 5 residues within 4Å: Chain D: H.118, E.137, R.140, R.141 Ligands: EDO.14 Ligand excluded by PLIP PO4.23: 5 residues within 4Å: Chain E: H.118, E.137, R.140, R.141 Chain G: K.190 Ligand excluded by PLIP PO4.26: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PO4.30: 5 residues within 4Å: Chain F: H.118, E.137, R.140, R.141 Ligands: EDO.24 Ligand excluded by PLIP PO4.33: 5 residues within 4Å: Chain E: K.190 Chain G: H.118, E.137, R.140, R.141 Ligand excluded by PLIP PO4.36: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PO4.40: 5 residues within 4Å: Chain H: H.118, E.137, R.140, R.141 Ligands: EDO.34 Ligand excluded by PLIP PO4.43: 5 residues within 4Å: Chain C: K.190 Chain I: H.118, E.137, R.140, R.141 Ligand excluded by PLIP PO4.46: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PO4.50: 5 residues within 4Å: Chain J: H.118, E.137, R.140, R.141 Ligands: EDO.44 Ligand excluded by PLIP PO4.53: 5 residues within 4Å: Chain A: K.190 Chain K: H.118, E.137, R.140, R.141 Ligand excluded by PLIP PO4.56: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP PO4.60: 5 residues within 4Å: Chain L: H.118, E.137, R.140, R.141 Ligands: EDO.54 Ligand excluded by PLIP

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

CL.7: 2 residues within 4Å: Chain B: A.58, G.59 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain D: A.58, G.59 Ligand excluded by PLIP CL.27: 2 residues within 4Å: Chain F: A.58, G.59 Ligand excluded by PLIP CL.37: 2 residues within 4Å: Chain H: A.58, G.59 Ligand excluded by PLIP CL.47: 2 residues within 4Å: Chain J: A.58, G.59 Ligand excluded by PLIP CL.57: 2 residues within 4Å: Chain L: A.58, G.59 Ligand excluded by PLIP

6 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PGE.19: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PGE.29: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PGE.39: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PGE.49: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PGE.59: 0 residues within 4Å: (No contacts) 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

2024-07-24

Peptides

Pyridoxal 5'-phosphate synthase subunit PdxS: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

I
A

J
B

K
A

L
B

Pyridoxal 5'-phosphate synthase subunit PdxS

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