SMTL ID : 2nv2.1

Structure of the PLP synthase complex Pdx1/2 (YaaD/E) from Bacillus subtilis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.12 Å

Oligo State

hetero-12-12-mer

Ligands

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

CL.1: 2 residues within 4Å: Chain A: R.137, R.138 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain C: R.137, R.138 Chain M: K.187 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain E: R.137, R.138 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain G: R.137, R.138 Chain U: K.187 Ligand excluded by PLIP CL.17: 2 residues within 4Å: Chain I: R.137, R.138 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain K: R.137, R.138 Chain Q: K.187 Ligand excluded by PLIP CL.25: 3 residues within 4Å: Chain C: K.187 Chain M: R.137, R.138 Ligand excluded by PLIP CL.28: 3 residues within 4Å: Chain A: K.187 Chain O: R.137, R.138 Ligand excluded by PLIP CL.30: 3 residues within 4Å: Chain K: K.187 Chain Q: R.137, R.138 Ligand excluded by PLIP CL.34: 3 residues within 4Å: Chain I: K.187 Chain S: R.137, R.138 Ligand excluded by PLIP CL.36: 3 residues within 4Å: Chain G: K.187 Chain U: R.137, R.138 Ligand excluded by PLIP CL.40: 2 residues within 4Å: Chain W: R.137, R.138 Ligand excluded by PLIP

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

EDO.2: 8 residues within 4Å: Chain A: A.186, K.187, A.191, P.192, Y.193 Chain O: G.190, P.192 Ligands: EDO.3 Ligand excluded by PLIP EDO.3: 9 residues within 4Å: Chain A: G.190, A.191, P.192 Chain O: A.186, K.187, A.191, P.192, Y.193 Ligands: EDO.2 Ligand excluded by PLIP EDO.4: 7 residues within 4Å: Chain A: P.192, Y.193, E.194, L.195 Chain O: P.192, Y.193, E.194 Ligand excluded by PLIP EDO.7: 9 residues within 4Å: Chain C: A.186, K.187, A.191, P.192, Y.193 Chain M: G.190, A.191, P.192 Ligands: EDO.8 Ligand excluded by PLIP EDO.8: 9 residues within 4Å: Chain C: G.190, A.191, P.192 Chain M: A.186, K.187, A.191, P.192, Y.193 Ligands: EDO.7 Ligand excluded by PLIP EDO.11: 10 residues within 4Å: Chain E: M.183, A.186, K.187, A.191, P.192, Y.193 Chain W: G.190, A.191, P.192 Ligands: EDO.41 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain E: P.192, Y.193, E.194, L.195 Chain W: P.192, Y.193, E.194 Ligand excluded by PLIP EDO.15: 7 residues within 4Å: Chain G: P.192, Y.193, E.194, L.195 Chain U: P.192, Y.193, E.194 Ligand excluded by PLIP EDO.18: 8 residues within 4Å: Chain I: A.186, K.187, A.191, P.192, Y.193 Chain S: G.190, P.192 Ligands: EDO.19 Ligand excluded by PLIP EDO.19: 8 residues within 4Å: Chain I: G.190, P.192 Chain S: A.186, K.187, A.191, P.192, Y.193 Ligands: EDO.18 Ligand excluded by PLIP EDO.20: 7 residues within 4Å: Chain I: P.192, Y.193, E.194, L.195 Chain S: P.192, Y.193, E.194 Ligand excluded by PLIP EDO.23: 10 residues within 4Å: Chain K: M.183, A.186, K.187, A.191, P.192, Y.193 Chain Q: G.190, A.191, P.192 Ligands: EDO.31 Ligand excluded by PLIP EDO.26: 7 residues within 4Å: Chain C: P.192, Y.193, E.194 Chain M: P.192, Y.193, E.194, L.195 Ligand excluded by PLIP EDO.31: 9 residues within 4Å: Chain K: G.190, P.192 Chain Q: M.183, A.186, K.187, A.191, P.192, Y.193 Ligands: EDO.23 Ligand excluded by PLIP EDO.32: 7 residues within 4Å: Chain K: P.192, Y.193, E.194 Chain Q: P.192, Y.193, E.194, L.195 Ligand excluded by PLIP EDO.37: 9 residues within 4Å: Chain G: A.186, K.187, A.191, P.192, Y.193 Chain U: G.190, A.191, P.192 Ligands: EDO.38 Ligand excluded by PLIP EDO.38: 10 residues within 4Å: Chain G: G.190, A.191, P.192 Chain U: M.183, A.186, K.187, A.191, P.192, Y.193 Ligands: EDO.37 Ligand excluded by PLIP EDO.41: 8 residues within 4Å: Chain E: G.190, P.192 Chain W: A.186, K.187, A.191, P.192, Y.193 Ligands: EDO.11 Ligand excluded by PLIP

12 x GLN: GLUTAMINE(Non-covalent)

GLN.5: 12 residues within 4Å: Chain B: G.46, G.47, E.48, S.49, C.79, A.80, I.83, R.106, N.107, I.134, R.135, N.170 12 PLIP interactions: 12 interactions with chain B, Hydrogen bonds: B:G.47, B:S.49, B:A.80, B:N.107, B:I.134 Water bridges: B:E.48, B:E.48, B:T.50, B:I.134, B:R.135, B:R.135 Salt bridges: B:R.106 GLN.9: 13 residues within 4Å: Chain C: M.16 Chain D: G.46, G.47, E.48, S.49, C.79, A.80, I.83, R.106, N.107, I.134, R.135, N.170 12 PLIP interactions: 12 interactions with chain D, Hydrogen bonds: D:G.47, D:S.49, D:A.80, D:N.107, D:N.107, D:N.170 Water bridges: D:T.50, D:R.106, D:I.134, D:R.135, D:R.135 Salt bridges: D:R.106 GLN.13: 13 residues within 4Å: Chain E: M.16 Chain F: G.46, G.47, E.48, S.49, C.79, A.80, I.83, R.106, N.107, I.134, R.135, N.170 14 PLIP interactions: 14 interactions with chain F, Hydrogen bonds: F:G.47, F:E.48, F:S.49, F:A.80, F:N.107, F:N.170 Water bridges: F:E.48, F:T.50, F:R.106, F:R.106, F:N.107, F:I.134, F:R.135 Salt bridges: F:R.106 GLN.16: 13 residues within 4Å: Chain G: M.16 Chain H: G.46, G.47, E.48, S.49, C.79, A.80, I.83, R.106, N.107, I.134, R.135, N.170 12 PLIP interactions: 12 interactions with chain H Hydrogen bonds: H:G.47, H:S.49, H:A.80, H:N.107, H:N.107, H:N.170 Water bridges: H:T.50, H:R.106, H:I.134, H:R.135, H:R.135 Salt bridges: H:R.106 GLN.21: 13 residues within 4Å: Chain I: M.16 Chain J: G.46, G.47, E.48, S.49, C.79, A.80, I.83, R.106, N.107, I.134, R.135, N.170 12 PLIP interactions: 12 interactions with chain J, Hydrogen bonds: J:G.47, J:S.49, J:A.80, J:N.107, J:N.107, J:N.170 Water bridges: J:E.48, J:R.106, J:I.134, J:R.135, J:R.135 Salt bridges: J:R.106 GLN.24: 13 residues within 4Å: Chain K: M.16 Chain L: G.46, G.47, E.48, S.49, C.79, A.80, I.83, R.106, N.107, I.134, R.135, N.170 12 PLIP interactions: 12 interactions with chain L, Hydrogen bonds: L:G.47, L:S.49, L:A.80, L:N.107, L:R.135, L:N.170 Water bridges: L:E.48, L:R.106, L:I.134, L:R.135, L:R.135 Salt bridges: L:R.106 GLN.27: 13 residues within 4Å: Chain M: M.16 Chain N: G.46, G.47, E.48, S.49, C.79, A.80, I.83, R.106, N.107, I.134, R.135, N.170 12 PLIP interactions: 12 interactions with chain N, Hydrogen bonds: N:G.47, N:S.49, N:A.80, N:N.107, N:N.107, N:N.170 Water bridges: N:E.48, N:R.106, N:I.134, N:R.135, N:R.135 Salt bridges: N:R.106 GLN.29: 13 residues within 4Å: Chain O: M.16 Chain P: G.46, G.47, E.48, S.49, C.79, A.80, I.83, R.106, N.107, I.134, R.135, N.170 13 PLIP interactions: 13 interactions with chain P, Hydrogen bonds: P:G.47, P:G.47, P:S.49, P:A.80, P:N.107, P:N.107, P:I.134 Water bridges: P:T.50, P:R.106, P:I.134, P:R.135, P:R.135 Salt bridges: P:R.106 GLN.33: 13 residues within 4Å: Chain Q: M.16 Chain R: G.46, G.47, E.48, S.49, C.79, A.80, I.83, R.106, N.107, I.134, R.135, N.170 13 PLIP interactions: 13 interactions with chain R, Hydrogen bonds: R:G.47, R:G.47, R:S.49, R:A.80, R:N.107, R:N.107, R:N.170 Water bridges: R:E.48, R:R.106, R:I.134, R:R.135, R:R.135 Salt bridges: R:R.106 GLN.35: 13 residues within 4Å: Chain S: M.16 Chain T: G.46, G.47, E.48, S.49, C.79, A.80, I.83, R.106, N.107, I.134, R.135, N.170 13 PLIP interactions: 12 interactions with chain T, 1 Ligand-Ligand interactions Hydrogen bonds: T:G.47, T:G.47, T:S.49, T:A.80, T:N.107, T:N.107, T:N.170 Water bridges: T:R.106, T:I.134, T:R.135, T:R.135, Q.35 Salt bridges: T:R.106 GLN.39: 13 residues within 4Å: Chain U: M.16 Chain V: G.46, G.47, E.48, S.49, C.79, A.80, I.83, R.106, N.107, I.134, R.135, N.170 11 PLIP interactions: 11 interactions with chain V, Hydrogen bonds: V:G.47, V:S.49, V:A.80, V:N.107, V:N.107, V:N.170 Water bridges: V:T.50, V:R.106, V:I.134, V:R.135 Salt bridges: V:R.106 GLN.42: 13 residues within 4Å: Chain W: M.16 Chain X: G.46, G.47, E.48, S.49, C.79, A.80, I.83, R.106, N.107, I.134, R.135, N.170 12 PLIP interactions: 11 interactions with chain X, 1 Ligand-Ligand interactions Hydrogen bonds: X:G.47, X:A.80, X:R.106, X:R.106, X:N.107, X:N.107, X:N.170 Water bridges: X:N.107, X:I.134, X:R.135, X:R.135, Q.42

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: ACEGIKMOQSUW
Glutamine amidotransferase subunit pdxT: BDFHJLNPRTVX

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

G
G

I
I

K
K

M
M

O
O

Q
Q

S
S

U
U

W
W

B
B

D
D

F
F

H
H

J
J

L
L

N
N

P
P

R
R

T
T

V
V

X
X

Pyridoxal biosynthesis lyase pdxS

Glutamine amidotransferase subunit pdxT