- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.80 Å
- Oligo State
- homo-12-mer
- Ligands
- 6 x CL: CHLORIDE ION(Non-functional Binders)
- 24 x SO4: SULFATE ION(Non-functional Binders)
SO4.2: 5 residues within 4Å:- Chain A: H.131, E.150, R.153, R.154
- Chain K: K.203
Ligand excluded by PLIPSO4.3: 11 residues within 4Å:- Chain A: P.65, K.165, E.167, A.168, G.169, G.229, G.230, V.250, G.251, S.252
- Ligands: 6R3.4
Ligand excluded by PLIPSO4.7: 5 residues within 4Å:- Chain B: H.131, E.150, R.153, R.154
- Chain J: K.203
Ligand excluded by PLIPSO4.8: 11 residues within 4Å:- Chain B: P.65, K.165, E.167, A.168, G.169, G.229, G.230, V.250, G.251, S.252
- Ligands: 6R3.9
Ligand excluded by PLIPSO4.12: 5 residues within 4Å:- Chain C: H.131, E.150, R.153, R.154
- Chain G: K.203
Ligand excluded by PLIPSO4.13: 11 residues within 4Å:- Chain C: P.65, K.165, E.167, A.168, G.169, G.229, G.230, V.250, G.251, S.252
- Ligands: 6R3.14
Ligand excluded by PLIPSO4.17: 5 residues within 4Å:- Chain D: H.131, E.150, R.153, R.154
- Chain L: K.203
Ligand excluded by PLIPSO4.18: 11 residues within 4Å:- Chain D: P.65, K.165, E.167, A.168, G.169, G.229, G.230, V.250, G.251, S.252
- Ligands: 6R3.19
Ligand excluded by PLIPSO4.22: 5 residues within 4Å:- Chain E: H.131, E.150, R.153, R.154
- Chain I: K.203
Ligand excluded by PLIPSO4.23: 11 residues within 4Å:- Chain E: P.65, K.165, E.167, A.168, G.169, G.229, G.230, V.250, G.251, S.252
- Ligands: 6R3.24
Ligand excluded by PLIPSO4.27: 5 residues within 4Å:- Chain F: H.131, E.150, R.153, R.154
- Chain H: K.203
Ligand excluded by PLIPSO4.28: 11 residues within 4Å:- Chain F: P.65, K.165, E.167, A.168, G.169, G.229, G.230, V.250, G.251, S.252
- Ligands: 6R3.29
Ligand excluded by PLIPSO4.31: 5 residues within 4Å:- Chain C: K.203
- Chain G: H.131, E.150, R.153, R.154
Ligand excluded by PLIPSO4.32: 10 residues within 4Å:- Chain G: P.65, K.165, E.167, A.168, G.169, G.229, G.230, G.251, S.252
- Ligands: 6R3.33
Ligand excluded by PLIPSO4.36: 10 residues within 4Å:- Chain H: P.65, K.165, E.167, A.168, G.169, G.229, G.230, G.251, S.252
- Ligands: 6R3.38
Ligand excluded by PLIPSO4.37: 5 residues within 4Å:- Chain F: K.203
- Chain H: H.131, E.150, R.153, R.154
Ligand excluded by PLIPSO4.39: 5 residues within 4Å:- Chain E: K.203
- Chain I: H.131, E.150, R.153, R.154
Ligand excluded by PLIPSO4.40: 10 residues within 4Å:- Chain I: P.65, K.165, E.167, A.168, G.169, G.229, G.230, G.251, S.252
- Ligands: 6R3.41
Ligand excluded by PLIPSO4.44: 10 residues within 4Å:- Chain J: P.65, K.165, E.167, A.168, G.169, G.229, G.230, G.251, S.252
- Ligands: 6R3.46
Ligand excluded by PLIPSO4.45: 5 residues within 4Å:- Chain B: K.203
- Chain J: H.131, E.150, R.153, R.154
Ligand excluded by PLIPSO4.47: 5 residues within 4Å:- Chain A: K.203
- Chain K: H.131, E.150, R.153, R.154
Ligand excluded by PLIPSO4.48: 10 residues within 4Å:- Chain K: P.65, K.165, E.167, A.168, G.169, G.229, G.230, G.251, S.252
- Ligands: 6R3.49
Ligand excluded by PLIPSO4.52: 10 residues within 4Å:- Chain L: P.65, K.165, E.167, A.168, G.169, G.229, G.230, G.251, S.252
- Ligands: 6R3.54
Ligand excluded by PLIPSO4.53: 5 residues within 4Å:- Chain D: K.203
- Chain L: H.131, E.150, R.153, R.154
Ligand excluded by PLIP- 12 x 6R3: 2-azanylpenta-1,4-dien-3-one(Covalent)
6R3.4: 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: SO4.3
5 PLIP interactions:5 interactions with chain A- Hydrophobic interactions: A:K.97, A:V.122, A:K.165
- Hydrogen bonds: A:D.118, A:D.118
6R3.9: 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: SO4.8
5 PLIP interactions:5 interactions with chain B- Hydrophobic interactions: B:K.97, B:V.122, B:K.165
- Hydrogen bonds: B:D.118, B:D.118
6R3.14: 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: SO4.13
5 PLIP interactions:5 interactions with chain C- Hydrophobic interactions: C:K.97, C:V.122, C:K.165
- Hydrogen bonds: C:D.118, C:D.118
6R3.19: 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: SO4.18
5 PLIP interactions:5 interactions with chain D- Hydrophobic interactions: D:K.97, D:V.122, D:K.165
- Hydrogen bonds: D:D.118, D:D.118
6R3.24: 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: SO4.23
5 PLIP interactions:5 interactions with chain E- Hydrophobic interactions: E:K.97, E:V.122, E:K.165
- Hydrogen bonds: E:D.118, E:D.118
6R3.29: 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: SO4.28
5 PLIP interactions:5 interactions with chain F- Hydrophobic interactions: F:K.97, F:V.122, F:K.165
- Hydrogen bonds: F:D.118, F:D.118
6R3.33: 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: SO4.32
4 PLIP interactions:4 interactions with chain G- Hydrophobic interactions: G:K.97, G:V.122, G:K.165
- Hydrogen bonds: G:D.118
6R3.38: 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: SO4.36
4 PLIP interactions:4 interactions with chain H- Hydrophobic interactions: H:K.97, H:V.122, H:K.165
- Hydrogen bonds: H:D.118
6R3.41: 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: SO4.40
4 PLIP interactions:4 interactions with chain I- Hydrophobic interactions: I:K.97, I:V.122, I:K.165
- Hydrogen bonds: I:D.118
6R3.46: 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: SO4.44
4 PLIP interactions:4 interactions with chain J- Hydrophobic interactions: J:K.97, J:V.122, J:K.165
- Hydrogen bonds: J:D.118
6R3.49: 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: SO4.48
4 PLIP interactions:4 interactions with chain K- Hydrophobic interactions: K:K.97, K:V.122, K:K.165
- Hydrogen bonds: K:D.118
6R3.54: 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
4 PLIP interactions:4 interactions with chain L- Hydrophobic interactions: L:K.97, L:V.122, L:K.165
- Hydrogen bonds: L:D.118
- 12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.5: 6 residues within 4Å:- Chain A: E.121, G.144, C.145, R.146, E.150, K.165
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:E.150
- Water bridges: A:E.150
EDO.6: 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.10: 6 residues within 4Å:- Chain B: E.121, G.144, C.145, R.146, E.150, K.165
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:E.150
- Water bridges: B:E.150
EDO.15: 6 residues within 4Å:- Chain C: E.121, G.144, C.145, R.146, E.150, K.165
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:E.150
- Water bridges: C:E.150
EDO.16: 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.20: 6 residues within 4Å:- Chain D: E.121, G.144, C.145, R.146, E.150, K.165
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:E.150
- Water bridges: D:E.150
EDO.25: 6 residues within 4Å:- Chain E: E.121, G.144, C.145, R.146, E.150, K.165
2 PLIP interactions:2 interactions with chain E- Hydrogen bonds: E:E.150
- Water bridges: E:E.150
EDO.26: 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.30: 6 residues within 4Å:- Chain F: E.121, G.144, C.145, R.146, E.150, K.165
2 PLIP interactions:2 interactions with chain F- Hydrogen bonds: F:E.150
- Water bridges: F:E.150
EDO.34: 3 residues within 4Å:- Chain G: E.62, S.78, D.79
3 PLIP interactions:3 interactions with chain G- Hydrogen bonds: G:D.79
- Water bridges: G:E.62, G:E.62
EDO.42: 3 residues within 4Å:- Chain I: E.62, S.78, D.79
3 PLIP interactions:3 interactions with chain I- Hydrogen bonds: I:D.79
- Water bridges: I:E.62, I:E.62
EDO.50: 3 residues within 4Å:- Chain K: E.62, S.78, D.79
3 PLIP interactions:3 interactions with chain K- Hydrogen bonds: K:D.79
- Water bridges: K:E.62, K:E.62
- 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
AB
BC
AD
BE
AF
BG
CH
DI
CJ
DK
CL
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.80 Å
- Oligo State
- homo-12-mer
- Ligands
- 6 x CL: CHLORIDE ION(Non-functional Binders)
- 24 x SO4: SULFATE ION(Non-functional Binders)
- 12 x 6R3: 2-azanylpenta-1,4-dien-3-one(Covalent)
- 12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 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
AB
BC
AD
BE
AF
BG
CH
DI
CJ
DK
CL
D