SMTL ID : 5k2z.1 (1 other biounit)

PDX1.3-adduct (Arabidopsis)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-12-mer

Ligands

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

SO4.1: 5 residues within 4Å: Chain A: H.131, E.150, R.153, R.154 Chain I: K.203 Ligand excluded by PLIP SO4.2: 10 residues within 4Å: Chain A: P.65, K.165, E.167, A.168, G.169, G.229, G.230, G.251, S.252 Ligands: 6R3.3 Ligand excluded by PLIP SO4.6: 10 residues within 4Å: Chain B: P.65, K.165, E.167, A.168, G.169, G.229, G.230, G.251, S.252 Ligands: 6R3.8 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: 5 residues within 4Å: Chain C: H.131, E.150, R.153, R.154 Chain K: K.203 Ligand excluded by PLIP SO4.10: 10 residues within 4Å: Chain C: P.65, K.165, E.167, A.168, G.169, G.229, G.230, G.251, S.252 Ligands: 6R3.11 Ligand excluded by PLIP SO4.14: 10 residues within 4Å: Chain D: P.65, K.165, E.167, A.168, G.169, G.229, G.230, G.251, S.252 Ligands: 6R3.16 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: 5 residues within 4Å: Chain E: H.131, E.150, R.153, R.154 Chain G: K.203 Ligand excluded by PLIP SO4.18: 10 residues within 4Å: Chain E: P.65, K.165, E.167, A.168, G.169, G.229, G.230, G.251, S.252 Ligands: 6R3.19 Ligand excluded by PLIP SO4.22: 10 residues within 4Å: Chain F: P.65, K.165, E.167, A.168, G.169, G.229, G.230, G.251, S.252 Ligands: 6R3.24 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 SO4.26: 5 residues within 4Å: Chain E: K.203 Chain G: H.131, E.150, R.153, R.154 Ligand excluded by PLIP SO4.27: 11 residues within 4Å: Chain G: P.65, K.165, E.167, A.168, G.169, G.229, G.230, V.250, G.251, S.252 Ligands: 6R3.28 Ligand excluded by PLIP SO4.31: 5 residues within 4Å: Chain D: K.203 Chain H: H.131, E.150, R.153, R.154 Ligand excluded by PLIP SO4.32: 11 residues within 4Å: Chain H: P.65, K.165, E.167, A.168, G.169, G.229, G.230, V.250, G.251, S.252 Ligands: 6R3.33 Ligand excluded by PLIP SO4.36: 5 residues within 4Å: Chain A: K.203 Chain I: H.131, E.150, R.153, R.154 Ligand excluded by PLIP SO4.37: 11 residues within 4Å: Chain I: P.65, K.165, E.167, A.168, G.169, G.229, G.230, V.250, G.251, S.252 Ligands: 6R3.38 Ligand excluded by PLIP SO4.41: 5 residues within 4Å: Chain F: K.203 Chain J: H.131, E.150, R.153, R.154 Ligand excluded by PLIP SO4.42: 11 residues within 4Å: Chain J: P.65, K.165, E.167, A.168, G.169, G.229, G.230, V.250, G.251, S.252 Ligands: 6R3.43 Ligand excluded by PLIP SO4.46: 5 residues within 4Å: Chain C: K.203 Chain K: H.131, E.150, R.153, R.154 Ligand excluded by PLIP SO4.47: 11 residues within 4Å: Chain K: P.65, K.165, E.167, A.168, G.169, G.229, G.230, V.250, G.251, S.252 Ligands: 6R3.48 Ligand excluded by PLIP SO4.51: 5 residues within 4Å: Chain B: K.203 Chain L: H.131, E.150, R.153, R.154 Ligand excluded by PLIP SO4.52: 11 residues within 4Å: Chain L: P.65, K.165, E.167, A.168, G.169, G.229, G.230, V.250, G.251, S.252 Ligands: 6R3.53 Ligand excluded by PLIP

12 x 6R3: 2-azanylpenta-1,4-dien-3-one(Covalent)

6R3.3: 10 residues within 4Å: Chain A: D.40, M.59, K.97, D.118, S.120, V.122, R.163, K.165, F.249 Ligands: SO4.2 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.97, A:V.122, A:K.165 Hydrogen bonds: A:D.118 6R3.8: 10 residues within 4Å: Chain B: D.40, M.59, K.97, D.118, S.120, V.122, R.163, K.165, F.249 Ligands: SO4.6 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:K.97, B:V.122, B:K.165 Hydrogen bonds: B:D.118 6R3.11: 10 residues within 4Å: Chain C: D.40, M.59, K.97, D.118, S.120, V.122, R.163, K.165, F.249 Ligands: SO4.10 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:K.97, C:V.122, C:K.165 Hydrogen bonds: C:D.118 6R3.16: 10 residues within 4Å: Chain D: D.40, M.59, K.97, D.118, S.120, V.122, R.163, K.165, F.249 Ligands: SO4.14 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:K.97, D:V.122, D:K.165 Hydrogen bonds: D:D.118 6R3.19: 10 residues within 4Å: Chain E: D.40, M.59, K.97, D.118, S.120, V.122, R.163, K.165, F.249 Ligands: SO4.18 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:K.97, E:V.122, E:K.165 Hydrogen bonds: E:D.118 6R3.24: 10 residues within 4Å: Chain F: D.40, M.59, K.97, D.118, S.120, V.122, R.163, K.165, F.249 Ligands: SO4.22 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:K.97, F:V.122, F:K.165 Hydrogen bonds: F:D.118 6R3.28: 10 residues within 4Å: Chain G: D.40, M.59, K.97, D.118, S.120, V.122, R.163, K.165, F.249 Ligands: SO4.27 5 PLIP interactions: 5 interactions with chain G Hydrophobic interactions: G:K.97, G:V.122, G:K.165 Hydrogen bonds: G:D.118, G:D.118 6R3.33: 10 residues within 4Å: Chain H: D.40, M.59, K.97, D.118, S.120, V.122, R.163, K.165, F.249 Ligands: SO4.32 5 PLIP interactions: 5 interactions with chain H Hydrophobic interactions: H:K.97, H:V.122, H:K.165 Hydrogen bonds: H:D.118, H:D.118 6R3.38: 10 residues within 4Å: Chain I: D.40, M.59, K.97, D.118, S.120, V.122, R.163, K.165, F.249 Ligands: SO4.37 5 PLIP interactions: 5 interactions with chain I Hydrophobic interactions: I:K.97, I:V.122, I:K.165 Hydrogen bonds: I:D.118, I:D.118 6R3.43: 10 residues within 4Å: Chain J: D.40, M.59, K.97, D.118, S.120, V.122, R.163, K.165, F.249 Ligands: SO4.42 5 PLIP interactions: 5 interactions with chain J Hydrophobic interactions: J:K.97, J:V.122, J:K.165 Hydrogen bonds: J:D.118, J:D.118 6R3.48: 10 residues within 4Å: Chain K: D.40, M.59, K.97, D.118, S.120, V.122, R.163, K.165, F.249 Ligands: SO4.47 5 PLIP interactions: 5 interactions with chain K Hydrophobic interactions: K:K.97, K:V.122, K:K.165 Hydrogen bonds: K:D.118, K:D.118 6R3.53: 10 residues within 4Å: Chain L: D.40, M.59, K.97, D.118, S.120, V.122, R.163, K.165, F.249 Ligands: SO4.52 5 PLIP interactions: 5 interactions with chain L Hydrophobic interactions: L:K.97, L:V.122, L:K.165 Hydrogen bonds: L:D.118, L:D.118

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

EDO.4: 3 residues within 4Å: Chain A: E.62, S.78, D.79 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.79 Water bridges: A:E.62, A:E.62 EDO.12: 3 residues within 4Å: Chain C: E.62, S.78, D.79 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.79 Water bridges: C:E.62, C:E.62 EDO.20: 3 residues within 4Å: Chain E: E.62, S.78, D.79 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:D.79 Water bridges: E:E.62, E:E.62 EDO.29: 6 residues within 4Å: Chain G: E.121, G.144, C.145, R.146, E.150, K.165 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:E.150 Water bridges: G:E.150 EDO.30: 7 residues within 4Å: Chain G: Q.31, R.34, R.220, L.221, P.222, V.223, V.224 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:Q.31, G:Q.31 EDO.34: 6 residues within 4Å: Chain H: E.121, G.144, C.145, R.146, E.150, K.165 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:E.150 Water bridges: H:E.150 EDO.39: 6 residues within 4Å: Chain I: E.121, G.144, C.145, R.146, E.150, K.165 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:E.150 Water bridges: I:E.150 EDO.40: 7 residues within 4Å: Chain I: Q.31, R.34, R.220, L.221, P.222, V.223, V.224 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:Q.31, I:Q.31 EDO.44: 6 residues within 4Å: Chain J: E.121, G.144, C.145, R.146, E.150, K.165 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:E.150 Water bridges: J:E.150 EDO.49: 6 residues within 4Å: Chain K: E.121, G.144, C.145, R.146, E.150, K.165 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:E.150 Water bridges: K:E.150 EDO.50: 7 residues within 4Å: Chain K: Q.31, R.34, R.220, L.221, P.222, V.223, V.224 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:Q.31, K:Q.31 EDO.54: 6 residues within 4Å: Chain L: E.121, G.144, C.145, R.146, E.150, K.165 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:E.150 Water bridges: L:E.150

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

CL.5: 2 residues within 4Å: Chain B: N.295 Chain C: L.125 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain D: N.295 Chain E: L.125 Ligand excluded by PLIP CL.21: 2 residues within 4Å: Chain A: L.125 Chain F: N.295 Ligand excluded by PLIP CL.25: 2 residues within 4Å: Chain G: N.295 Chain H: L.125 Ligand excluded by PLIP CL.35: 2 residues within 4Å: Chain I: N.295 Chain J: L.125 Ligand excluded by PLIP CL.45: 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
C

B
D

C
C

D
D

E
C

F
D

G
A

H
B

I
A

J
B

K
A

L
B

Pyridoxal 5'-phosphate synthase subunit PDX1.3

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