SMTL ID : 2nv1.1

Structure of the synthase subunit Pdx1 (YaaD) of PLP synthase from Bacillus subtilis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.08 Å

Oligo State

homo-12-mer

Ligands

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

CL.1: 2 residues within 4Å: Chain A: R.140, R.141 Ligand excluded by PLIP CL.2: 3 residues within 4Å: Chain A: G.156, G.216, G.217 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain B: R.140, R.141 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain B: G.156, G.216, G.217 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain C: R.140, R.141 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain C: G.156, G.216, G.217 Ligand excluded by PLIP CL.21: 2 residues within 4Å: Chain D: R.140, R.141 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain D: G.156, G.216, G.217 Ligand excluded by PLIP CL.26: 2 residues within 4Å: Chain E: R.140, R.141 Ligand excluded by PLIP CL.27: 4 residues within 4Å: Chain E: P.155, G.156, G.216, G.217 Ligand excluded by PLIP CL.31: 2 residues within 4Å: Chain F: R.140, R.141 Ligand excluded by PLIP CL.32: 3 residues within 4Å: Chain F: G.156, G.216, G.217 Ligand excluded by PLIP CL.36: 2 residues within 4Å: Chain G: R.140, R.141 Ligand excluded by PLIP CL.37: 3 residues within 4Å: Chain G: G.156, G.216, G.217 Ligand excluded by PLIP CL.43: 2 residues within 4Å: Chain H: R.140, R.141 Ligand excluded by PLIP CL.44: 3 residues within 4Å: Chain H: G.156, G.216, G.217 Ligand excluded by PLIP CL.48: 2 residues within 4Å: Chain I: R.140, R.141 Ligand excluded by PLIP CL.49: 3 residues within 4Å: Chain I: G.156, G.216, G.217 Ligand excluded by PLIP CL.56: 2 residues within 4Å: Chain J: R.140, R.141 Ligand excluded by PLIP CL.57: 3 residues within 4Å: Chain J: G.156, G.216, G.217 Ligand excluded by PLIP CL.61: 2 residues within 4Å: Chain K: R.140, R.141 Ligand excluded by PLIP CL.62: 4 residues within 4Å: Chain K: P.155, G.156, G.216, G.217 Ligand excluded by PLIP CL.66: 2 residues within 4Å: Chain L: R.140, R.141 Ligand excluded by PLIP CL.67: 3 residues within 4Å: Chain L: G.156, G.216, G.217 Ligand excluded by PLIP

24 x MG: MAGNESIUM ION(Non-functional Binders)

MG.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.5: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.23: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.24: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.28: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.29: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.33: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.38: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.39: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.40: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.45: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.50: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.51: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.52: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.58: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.59: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.63: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.64: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.68: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

EDO.6: 10 residues within 4Å: Chain A: M.186, A.189, K.190, A.194, P.195, Y.196 Chain G: G.193, A.194, P.195 Ligands: EDO.41 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: K.190 Chain G: R.140, K.190, N.191, G.193 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain B: K.190 Chain L: K.190, N.191, L.192, G.193 Ligand excluded by PLIP EDO.12: 9 residues within 4Å: Chain B: A.189, K.190, A.194, P.195, Y.196 Chain L: R.140, G.193, P.195 Ligands: EDO.70 Ligand excluded by PLIP EDO.18: 7 residues within 4Å: Chain C: P.195, Y.196, E.197, L.198 Chain K: P.195, Y.196, E.197 Ligand excluded by PLIP EDO.19: 9 residues within 4Å: Chain C: A.189, K.190, A.194, P.195, Y.196 Chain K: G.193, A.194, P.195 Ligands: EDO.65 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain C: D.27, M.46, K.84, D.105, R.150, F.236 Ligand excluded by PLIP EDO.25: 10 residues within 4Å: Chain D: A.189, K.190, A.194, P.195, Y.196 Chain J: R.140, G.193, A.194, P.195 Ligands: EDO.60 Ligand excluded by PLIP EDO.30: 9 residues within 4Å: Chain E: A.189, K.190, A.194, P.195, Y.196 Chain I: G.193, A.194, P.195 Ligands: EDO.54 Ligand excluded by PLIP EDO.34: 8 residues within 4Å: Chain F: P.195, Y.196, E.197, L.198 Chain H: P.195, Y.196, E.197, L.198 Ligand excluded by PLIP EDO.35: 10 residues within 4Å: Chain F: M.186, A.189, K.190, A.194, P.195, Y.196 Chain H: G.193, A.194, P.195 Ligands: EDO.47 Ligand excluded by PLIP EDO.41: 10 residues within 4Å: Chain A: G.193, A.194, P.195 Chain G: M.186, A.189, K.190, A.194, P.195, Y.196 Ligands: EDO.6 Ligand excluded by PLIP EDO.42: 5 residues within 4Å: Chain A: R.140, K.190, N.191, G.193 Chain G: K.190 Ligand excluded by PLIP EDO.46: 5 residues within 4Å: Chain F: K.190, N.191, L.192, G.193 Chain H: K.190 Ligand excluded by PLIP EDO.47: 9 residues within 4Å: Chain F: R.140, G.193, P.195 Chain H: A.189, K.190, A.194, P.195, Y.196 Ligands: EDO.35 Ligand excluded by PLIP EDO.53: 7 residues within 4Å: Chain E: P.195, Y.196, E.197 Chain I: P.195, Y.196, E.197, L.198 Ligand excluded by PLIP EDO.54: 9 residues within 4Å: Chain E: G.193, A.194, P.195 Chain I: A.189, K.190, A.194, P.195, Y.196 Ligands: EDO.30 Ligand excluded by PLIP EDO.55: 6 residues within 4Å: Chain I: D.27, M.46, K.84, D.105, R.150, F.236 Ligand excluded by PLIP EDO.60: 10 residues within 4Å: Chain D: R.140, G.193, A.194, P.195 Chain J: A.189, K.190, A.194, P.195, Y.196 Ligands: EDO.25 Ligand excluded by PLIP EDO.65: 9 residues within 4Å: Chain C: G.193, A.194, P.195 Chain K: A.189, K.190, A.194, P.195, Y.196 Ligands: EDO.19 Ligand excluded by PLIP EDO.69: 8 residues within 4Å: Chain B: P.195, Y.196, E.197, L.198 Chain L: P.195, Y.196, E.197, L.198 Ligand excluded by PLIP EDO.70: 10 residues within 4Å: Chain B: G.193, A.194, P.195 Chain L: M.186, A.189, K.190, A.194, P.195, Y.196 Ligands: EDO.12 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Strohmeier, M. et al., Structure of a bacterial pyridoxal 5'-phosphate synthase complex. Proc.Natl.Acad.Sci.Usa (2006)

Release Date

2006-12-05

Peptides

Pyridoxal biosynthesis lyase pdxS: 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

Pyridoxal biosynthesis lyase pdxS