SMTL ID : 7nhf.1

Crystal structure of Arabidopsis thaliana Pdx1K166R

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-12-mer

Ligands

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

PO4.1: 5 residues within 4Å: Chain A: H.131, E.150, R.153, R.154 Chain D: K.203 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Salt bridges: A:H.131, A:R.153, A:R.154, D:K.203 PO4.2: 5 residues within 4Å: Chain B: H.131, E.150, R.153, R.154 Chain C: K.203 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain B Salt bridges: C:K.203, B:H.131, B:R.153, B:R.154 Water bridges: B:R.146 PO4.3: 3 residues within 4Å: Chain B: K.203 Chain C: R.153, R.154 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Salt bridges: C:H.131, C:R.153, C:R.154, B:K.203 PO4.4: 4 residues within 4Å: Chain A: K.203 Chain D: H.131, R.153, R.154 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain A Salt bridges: D:H.131, D:R.153, D:R.154, A:K.203 PO4.5: 5 residues within 4Å: Chain E: H.131, E.150, R.153, R.154 Chain H: K.203 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain H Salt bridges: E:H.131, E:R.153, E:R.154, H:K.203 PO4.6: 5 residues within 4Å: Chain F: H.131, E.150, R.153, R.154 Chain G: K.203 5 PLIP interactions: 4 interactions with chain F, 1 interactions with chain G Water bridges: F:R.146 Salt bridges: F:H.131, F:R.153, F:R.154, G:K.203 PO4.7: 3 residues within 4Å: Chain F: K.203 Chain G: R.153, R.154 4 PLIP interactions: 3 interactions with chain G, 1 interactions with chain F Salt bridges: G:H.131, G:R.153, G:R.154, F:K.203 PO4.8: 4 residues within 4Å: Chain E: K.203 Chain H: H.131, R.153, R.154 4 PLIP interactions: 3 interactions with chain H, 1 interactions with chain E Salt bridges: H:H.131, H:R.153, H:R.154, E:K.203 PO4.9: 5 residues within 4Å: Chain I: H.131, E.150, R.153, R.154 Chain L: K.203 4 PLIP interactions: 3 interactions with chain I, 1 interactions with chain L Salt bridges: I:H.131, I:R.153, I:R.154, L:K.203 PO4.10: 5 residues within 4Å: Chain J: H.131, E.150, R.153, R.154 Chain K: K.203 5 PLIP interactions: 4 interactions with chain J, 1 interactions with chain K Water bridges: J:R.146 Salt bridges: J:H.131, J:R.153, J:R.154, K:K.203 PO4.11: 3 residues within 4Å: Chain J: K.203 Chain K: R.153, R.154 4 PLIP interactions: 1 interactions with chain J, 3 interactions with chain K Salt bridges: J:K.203, K:H.131, K:R.153, K:R.154 PO4.12: 4 residues within 4Å: Chain I: K.203 Chain L: H.131, R.153, R.154 4 PLIP interactions: 3 interactions with chain L, 1 interactions with chain I Salt bridges: L:H.131, L:R.153, L:R.154, I:K.203

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rodrigues, M.J. et al., Trapping and structural characterisation of a covalent intermediate in vitamin B 6 biosynthesis catalysed by the Pdx1 PLP synthase. Rsc Chem Biol (2022)

Release Date

2021-12-22

Peptides

Pyridoxal 5'-phosphate synthase subunit PDX1.3: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

I
A

J
B

K
C

L
D

Pyridoxal 5'-phosphate synthase subunit PDX1.3

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