SMTL ID : 5k3v.2 (1 other biounit)

apo-PDX1.3 (Arabidopsis)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-12-mer

Ligands

24 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 8 residues within 4Å: Chain A: P.65, E.167, A.168, G.169, G.229, G.230, G.251, S.252 Ligand excluded by PLIP SO4.2: 5 residues within 4Å: Chain A: H.131, E.150, R.153, R.154 Chain I: K.203 Ligand excluded by PLIP SO4.6: 8 residues within 4Å: Chain B: P.65, E.167, A.168, G.169, G.229, G.230, G.251, S.252 Ligand excluded by PLIP SO4.7: 5 residues within 4Å: Chain B: H.131, E.150, R.153, R.154 Chain L: K.203 Ligand excluded by PLIP SO4.9: 8 residues within 4Å: Chain C: P.65, E.167, A.168, G.169, G.229, G.230, G.251, S.252 Ligand excluded by PLIP SO4.10: 5 residues within 4Å: Chain C: H.131, E.150, R.153, R.154 Chain K: K.203 Ligand excluded by PLIP SO4.14: 8 residues within 4Å: Chain D: P.65, E.167, A.168, G.169, G.229, G.230, G.251, S.252 Ligand excluded by PLIP SO4.15: 5 residues within 4Å: Chain D: H.131, E.150, R.153, R.154 Chain H: K.203 Ligand excluded by PLIP SO4.17: 8 residues within 4Å: Chain E: P.65, E.167, A.168, G.169, G.229, G.230, G.251, S.252 Ligand excluded by PLIP SO4.18: 5 residues within 4Å: Chain E: H.131, E.150, R.153, R.154 Chain G: K.203 Ligand excluded by PLIP SO4.22: 8 residues within 4Å: Chain F: P.65, E.167, A.168, G.169, G.229, G.230, G.251, S.252 Ligand excluded by PLIP SO4.23: 5 residues within 4Å: Chain F: H.131, E.150, R.153, R.154 Chain J: K.203 Ligand excluded by PLIP SO4.25: 9 residues within 4Å: Chain G: P.65, A.168, G.169, G.229, G.230, V.231, G.251, S.252, G.253 Ligand excluded by PLIP SO4.26: 5 residues within 4Å: Chain E: K.203 Chain G: H.131, E.150, R.153, R.154 Ligand excluded by PLIP SO4.28: 8 residues within 4Å: Chain H: P.65, E.167, A.168, G.169, G.229, G.230, G.251, S.252 Ligand excluded by PLIP SO4.29: 5 residues within 4Å: Chain D: K.203 Chain H: H.131, E.150, R.153, R.154 Ligand excluded by PLIP SO4.33: 9 residues within 4Å: Chain I: P.65, A.168, G.169, G.229, G.230, V.231, G.251, S.252, G.253 Ligand excluded by PLIP SO4.34: 5 residues within 4Å: Chain A: K.203 Chain I: H.131, E.150, R.153, R.154 Ligand excluded by PLIP SO4.36: 8 residues within 4Å: Chain J: P.65, E.167, A.168, G.169, G.229, G.230, G.251, S.252 Ligand excluded by PLIP SO4.37: 5 residues within 4Å: Chain F: K.203 Chain J: H.131, E.150, R.153, R.154 Ligand excluded by PLIP SO4.41: 9 residues within 4Å: Chain K: P.65, A.168, G.169, G.229, G.230, V.231, G.251, S.252, G.253 Ligand excluded by PLIP SO4.42: 5 residues within 4Å: Chain C: K.203 Chain K: H.131, E.150, R.153, R.154 Ligand excluded by PLIP SO4.44: 8 residues within 4Å: Chain L: P.65, E.167, A.168, G.169, G.229, G.230, G.251, S.252 Ligand excluded by PLIP SO4.45: 5 residues within 4Å: Chain B: K.203 Chain L: H.131, E.150, R.153, R.154 Ligand excluded by PLIP

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

EDO.3: 7 residues within 4Å: Chain A: Q.31, R.34, R.220, L.221, P.222, V.223, V.224 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.31, A:Q.31 EDO.8: 7 residues within 4Å: Chain B: Q.31, R.34, R.220, L.221, P.222, V.223, V.224 No protein-ligand interaction detected (PLIP) EDO.11: 7 residues within 4Å: Chain C: Q.31, R.34, R.220, L.221, P.222, V.223, V.224 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.31, C:Q.31 EDO.16: 7 residues within 4Å: Chain D: Q.31, R.34, R.220, L.221, P.222, V.223, V.224 No protein-ligand interaction detected (PLIP) EDO.19: 7 residues within 4Å: Chain E: Q.31, R.34, R.220, L.221, P.222, V.223, V.224 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:Q.31, E:Q.31 EDO.24: 7 residues within 4Å: Chain F: Q.31, R.34, R.220, L.221, P.222, V.223, V.224 No protein-ligand interaction detected (PLIP) EDO.27: 6 residues within 4Å: Chain G: Q.31, R.220, L.221, P.222, V.223, V.224 1 PLIP interactions: 1 interactions with chain G Water bridges: G:V.224 EDO.35: 6 residues within 4Å: Chain I: Q.31, R.220, L.221, P.222, V.223, V.224 1 PLIP interactions: 1 interactions with chain I Water bridges: I:V.224 EDO.43: 6 residues within 4Å: Chain K: Q.31, R.220, L.221, P.222, V.223, V.224 1 PLIP interactions: 1 interactions with chain K Water bridges: K:V.224

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

CL.4: 2 residues within 4Å: Chain A: N.295 Chain B: L.125 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: L.125 Chain F: N.295 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain C: N.295 Chain D: L.125 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain B: N.295 Chain C: L.125 Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain E: N.295 Chain F: L.125 Ligand excluded by PLIP CL.21: 2 residues within 4Å: Chain D: N.295 Chain E: L.125 Ligand excluded by PLIP CL.30: 6 residues within 4Å: Chain D: P.208, Y.209, D.210 Chain H: P.208, Y.209, D.210 Ligand excluded by PLIP CL.31: 2 residues within 4Å: Chain H: N.295 Chain K: L.125 Ligand excluded by PLIP CL.32: 2 residues within 4Å: Chain G: N.295 Chain H: L.125 Ligand excluded by PLIP CL.38: 6 residues within 4Å: Chain F: P.208, Y.209, D.210 Chain J: P.208, Y.209, D.210 Ligand excluded by PLIP CL.39: 2 residues within 4Å: Chain G: L.125 Chain J: N.295 Ligand excluded by PLIP CL.40: 2 residues within 4Å: Chain I: N.295 Chain J: L.125 Ligand excluded by PLIP CL.46: 6 residues within 4Å: Chain B: P.208, Y.209, D.210 Chain L: P.208, Y.209, D.210 Ligand excluded by PLIP CL.47: 2 residues within 4Å: Chain I: L.125 Chain L: N.295 Ligand excluded by PLIP CL.48: 2 residues within 4Å: Chain K: N.295 Chain L: L.125 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Robinson, G.C. et al., Structural definition of the lysine swing in Arabidopsis thaliana PDX1: Intermediate channeling facilitating vitamin B6 biosynthesis. Proc.Natl.Acad.Sci.USA (2016)

Release Date

2016-10-05

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
A

D
C

E
A

F
C

G
B

H
D

I
B

J
D

K
B

L
D

Pyridoxal 5'-phosphate synthase subunit PDX1.3

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