SMTL ID : 4wy0.1

PdxS (G. stearothermophilus) co-crystallized with R5P in the presence of ammonia.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-8-3-1-mer

Ligands

5 x CAC: CACODYLATE ION(Non-covalent)

CAC.1: 5 residues within 4Å: Chain A: H.125, E.144, R.147, R.148 Chain G: K.197 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.147, A:R.148, A:R.148 CAC.4: 5 residues within 4Å: Chain C: H.125, E.144, R.147, R.148 Chain H: K.197 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain C Water bridges: H:K.197 Hydrogen bonds: C:R.147 CAC.10: 5 residues within 4Å: Chain F: H.125, E.144, R.147, R.148 Chain K: K.197 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:H.125, F:R.147, F:R.148, F:R.148 CAC.15: 4 residues within 4Å: Chain C: K.197 Chain H: H.125, R.147, R.148 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:R.147 CAC.19: 4 residues within 4Å: Chain D: K.197 Chain L: H.125, R.147, R.148 3 PLIP interactions: 3 interactions with chain L Hydrogen bonds: L:R.147, L:R.148, L:R.148

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

PO4.2: 4 residues within 4Å: Chain B: G.163, G.223, G.224, G.245 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.163, B:G.224, B:G.245 Water bridges: B:G.223, B:G.223 Salt bridges: B:K.159 PO4.6: 5 residues within 4Å: Chain D: P.162, G.163, G.223, G.224, G.245 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:G.163, D:G.224, D:G.245 Water bridges: D:T.164, D:G.223, D:G.223, D:G.245 PO4.9: 5 residues within 4Å: Chain F: X.91, P.162, G.163, G.224, G.245 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:G.163, F:G.224, F:G.245 Water bridges: F:G.223, F:V.225 PO4.14: 4 residues within 4Å: Chain H: G.163, G.224, V.225, G.245 7 PLIP interactions: 7 interactions with chain H Hydrogen bonds: H:G.163, H:G.224, H:G.245 Water bridges: H:T.164, H:G.223, H:V.225, H:G.245

7 x R5P: RIBOSE-5-PHOSPHATE(Non-covalent)

R5P.3: 6 residues within 4Å: Chain B: H.125, R.140, E.144, R.147, R.148 Chain J: K.197 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain J Water bridges: B:R.140, B:R.140, B:R.140, B:E.144 Salt bridges: B:H.125, B:R.147, B:R.148, J:K.197 R5P.7: 7 residues within 4Å: Chain D: E.115, H.125, R.140, E.144, R.147, R.148 Chain L: K.197 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain L Hydrogen bonds: D:R.140, D:R.140 Water bridges: D:R.148 Salt bridges: D:H.125, D:R.147, D:R.148, L:K.197 R5P.8: 8 residues within 4Å: Chain E: I.94, P.119, H.125, R.140, E.144, R.147, R.148 Chain I: K.197 11 PLIP interactions: 10 interactions with chain E, 1 interactions with chain I Hydrogen bonds: E:R.140 Water bridges: E:E.122, E:H.125, E:E.144, E:R.147, E:R.147, E:R.148 Salt bridges: E:H.125, E:R.147, E:R.148, I:K.197 R5P.11: 8 residues within 4Å: Chain A: K.197 Chain G: I.94, H.125, R.140, E.144, R.147, R.148 Ligands: EDO.12 8 PLIP interactions: 1 interactions with chain A, 7 interactions with chain G Salt bridges: A:K.197, G:H.125, G:R.147, G:R.148 Water bridges: G:H.125, G:R.140, G:R.147, G:E.151 R5P.16: 7 residues within 4Å: Chain E: K.197 Chain I: E.115, H.125, R.140, E.144, R.147, R.148 8 PLIP interactions: 7 interactions with chain I, 1 interactions with chain E Hydrogen bonds: I:R.140, I:R.140 Water bridges: I:R.148, I:R.148 Salt bridges: I:H.125, I:R.147, I:R.148, E:K.197 R5P.17: 8 residues within 4Å: Chain B: K.197 Chain J: I.94, E.115, H.125, R.140, E.144, R.147, R.148 10 PLIP interactions: 9 interactions with chain J, 1 interactions with chain B Hydrogen bonds: J:R.140, J:R.140, J:E.144, J:R.148 Water bridges: J:E.144, J:E.144 Salt bridges: J:H.125, J:R.147, J:R.148, B:K.197 R5P.18: 7 residues within 4Å: Chain F: K.197 Chain K: E.115, H.125, R.140, E.144, R.147, R.148 11 PLIP interactions: 2 interactions with chain F, 9 interactions with chain K Water bridges: F:K.197, K:E.115, K:H.125, K:R.147, K:R.148 Salt bridges: F:K.197, K:H.125, K:R.147, K:R.148 Hydrogen bonds: K:R.140, K:R.140

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

EDO.5: 7 residues within 4Å: Chain C: G.95, D.121, F.124, H.125, I.126 Chain H: D.190 Chain K: R.175 4 PLIP interactions: 1 interactions with chain H, 2 interactions with chain C, 1 interactions with chain K Water bridges: H:D.190, C:D.127 Hydrogen bonds: C:D.121, K:R.175 EDO.12: 8 residues within 4Å: Chain G: I.94, E.115, H.125, G.138, C.139, E.144, R.148 Ligands: R5P.11 4 PLIP interactions: 4 interactions with chain G Hydrogen bonds: G:E.115, G:E.144, G:E.144, G:R.148 EDO.13: 7 residues within 4Å: Chain A: R.147, G.200, A.201 Chain G: V.193, A.196, K.197, A.201 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain A Hydrogen bonds: G:K.197, A:G.200

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Smith, A.M. et al., Crystal structures capture three states in the catalytic cycle of a pyridoxal phosphate (PLP) synthase. J.Biol.Chem. (2015)

Release Date

2015-01-14

Peptides

Pyridoxal biosynthesis lyase PdxS: ACEGIJKL
Pyridoxal biosynthesis lyase PdxS: BDH
Pyridoxal biosynthesis lyase PdxS: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

G
G

I
I

J
J

K
K

L
L

B
B

D
D

H
H

F
F

Pyridoxal biosynthesis lyase PdxS

Pyridoxal biosynthesis lyase PdxS

Pyridoxal biosynthesis lyase PdxS

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