- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.73 Å
- Oligo State
- homo-12-mer
- Ligands
- 12 x PO4: PHOSPHATE ION(Non-functional Binders)
- 12 x SO4: SULFATE ION(Non-functional Binders)
SO4.2: 5 residues within 4Å:- Chain A: H.131, E.150, R.153, R.154
- Chain D: K.203
10 PLIP interactions:7 interactions with chain A, 3 interactions with chain D- Water bridges: A:D.129, A:H.131, A:R.153, A:R.154, D:K.203, D:K.203
- Salt bridges: A:H.131, A:R.153, A:R.154, D:K.203
SO4.5: 5 residues within 4Å:- Chain B: H.131, E.150, R.153, R.154
- Chain C: K.203
8 PLIP interactions:6 interactions with chain B, 2 interactions with chain C- Water bridges: B:D.129, B:H.131, B:R.153, C:K.203
- Salt bridges: B:H.131, B:R.153, B:R.154, C:K.203
SO4.8: 5 residues within 4Å:- Chain B: K.203
- Chain C: H.131, E.150, R.153, R.154
9 PLIP interactions:2 interactions with chain B, 7 interactions with chain C- Water bridges: B:K.203, C:H.131, C:H.131, C:R.146, C:E.150
- Salt bridges: B:K.203, C:H.131, C:R.153, C:R.154
SO4.11: 5 residues within 4Å:- Chain A: K.203
- Chain D: H.131, E.150, R.153, R.154
10 PLIP interactions:8 interactions with chain D, 2 interactions with chain A- Water bridges: D:H.131, D:H.131, D:H.131, D:E.150, D:R.153, A:K.203
- Salt bridges: D:H.131, D:R.153, D:R.154, A:K.203
SO4.14: 5 residues within 4Å:- Chain E: H.131, E.150, R.153, R.154
- Chain H: K.203
10 PLIP interactions:7 interactions with chain E, 3 interactions with chain H- Water bridges: E:D.129, E:H.131, E:R.153, E:R.154, H:K.203, H:K.203
- Salt bridges: E:H.131, E:R.153, E:R.154, H:K.203
SO4.17: 5 residues within 4Å:- Chain F: H.131, E.150, R.153, R.154
- Chain G: K.203
8 PLIP interactions:6 interactions with chain F, 2 interactions with chain G- Water bridges: F:D.129, F:H.131, F:R.153, G:K.203
- Salt bridges: F:H.131, F:R.153, F:R.154, G:K.203
SO4.20: 5 residues within 4Å:- Chain F: K.203
- Chain G: H.131, E.150, R.153, R.154
9 PLIP interactions:7 interactions with chain G, 2 interactions with chain F- Water bridges: G:H.131, G:H.131, G:R.146, G:E.150, F:K.203
- Salt bridges: G:H.131, G:R.153, G:R.154, F:K.203
SO4.23: 5 residues within 4Å:- Chain E: K.203
- Chain H: H.131, E.150, R.153, R.154
10 PLIP interactions:8 interactions with chain H, 2 interactions with chain E- Water bridges: H:H.131, H:H.131, H:H.131, H:E.150, H:R.153, E:K.203
- Salt bridges: H:H.131, H:R.153, H:R.154, E:K.203
SO4.26: 5 residues within 4Å:- Chain I: H.131, E.150, R.153, R.154
- Chain L: K.203
10 PLIP interactions:3 interactions with chain L, 7 interactions with chain I- Water bridges: L:K.203, L:K.203, I:D.129, I:H.131, I:R.153, I:R.154
- Salt bridges: L:K.203, I:H.131, I:R.153, I:R.154
SO4.29: 5 residues within 4Å:- Chain J: H.131, E.150, R.153, R.154
- Chain K: K.203
8 PLIP interactions:6 interactions with chain J, 2 interactions with chain K- Water bridges: J:D.129, J:H.131, J:R.153, K:K.203
- Salt bridges: J:H.131, J:R.153, J:R.154, K:K.203
SO4.32: 5 residues within 4Å:- Chain J: K.203
- Chain K: H.131, E.150, R.153, R.154
9 PLIP interactions:2 interactions with chain J, 7 interactions with chain K- Water bridges: J:K.203, K:H.131, K:H.131, K:R.146, K:E.150
- Salt bridges: J:K.203, K:H.131, K:R.153, K:R.154
SO4.35: 5 residues within 4Å:- Chain I: K.203
- Chain L: H.131, E.150, R.153, R.154
10 PLIP interactions:8 interactions with chain L, 2 interactions with chain I- Water bridges: L:H.131, L:H.131, L:H.131, L:R.146, L:R.153, I:K.203
- Salt bridges: L:H.131, L:R.153, L:R.154, I:K.203
- 12 x KIK: (4~{S})-4-azanyl-5-oxidanyl-pent-1-en-3-one(Covalent)
KIK.3: 9 residues within 4Å:- Chain A: D.40, L.61, K.97, S.120, V.122, R.163, K.165, F.249
- Ligands: PO4.1
5 PLIP interactions:5 interactions with chain A- Hydrophobic interactions: A:L.61, A:K.97, A:V.122, A:K.165
- Hydrogen bonds: A:D.40
KIK.6: 9 residues within 4Å:- Chain B: D.40, L.61, K.97, S.120, V.122, R.163, K.165, F.249
- Ligands: PO4.4
5 PLIP interactions:5 interactions with chain B- Hydrophobic interactions: B:L.61, B:K.97, B:V.122, B:K.165
- Hydrogen bonds: B:D.40
KIK.9: 9 residues within 4Å:- Chain C: D.40, L.61, K.97, S.120, V.122, R.163, K.165, F.249
- Ligands: PO4.7
6 PLIP interactions:6 interactions with chain C- Hydrophobic interactions: C:L.61, C:K.97, C:V.122, C:K.165
- Hydrogen bonds: C:D.40, C:K.97
KIK.12: 9 residues within 4Å:- Chain D: D.40, L.61, K.97, S.120, V.122, R.163, K.165, F.249
- Ligands: PO4.10
6 PLIP interactions:6 interactions with chain D- Hydrophobic interactions: D:L.61, D:K.97, D:V.122, D:K.165
- Hydrogen bonds: D:D.40, D:K.97
KIK.15: 9 residues within 4Å:- Chain E: D.40, L.61, K.97, S.120, V.122, R.163, K.165, F.249
- Ligands: PO4.13
5 PLIP interactions:5 interactions with chain E- Hydrophobic interactions: E:L.61, E:K.97, E:V.122, E:K.165
- Hydrogen bonds: E:D.40
KIK.18: 9 residues within 4Å:- Chain F: D.40, L.61, K.97, S.120, V.122, R.163, K.165, F.249
- Ligands: PO4.16
5 PLIP interactions:5 interactions with chain F- Hydrophobic interactions: F:L.61, F:K.97, F:V.122, F:K.165
- Hydrogen bonds: F:D.40
KIK.21: 9 residues within 4Å:- Chain G: D.40, L.61, K.97, S.120, V.122, R.163, K.165, F.249
- Ligands: PO4.19
6 PLIP interactions:6 interactions with chain G- Hydrophobic interactions: G:L.61, G:K.97, G:V.122, G:K.165
- Hydrogen bonds: G:D.40, G:K.97
KIK.24: 9 residues within 4Å:- Chain H: D.40, L.61, K.97, S.120, V.122, R.163, K.165, F.249
- Ligands: PO4.22
6 PLIP interactions:6 interactions with chain H- Hydrophobic interactions: H:L.61, H:K.97, H:V.122, H:K.165
- Hydrogen bonds: H:D.40, H:K.97
KIK.27: 9 residues within 4Å:- Chain I: D.40, L.61, K.97, S.120, V.122, R.163, K.165, F.249
- Ligands: PO4.25
5 PLIP interactions:5 interactions with chain I- Hydrophobic interactions: I:L.61, I:K.97, I:V.122, I:K.165
- Hydrogen bonds: I:D.40
KIK.30: 9 residues within 4Å:- Chain J: D.40, L.61, K.97, S.120, V.122, R.163, K.165, F.249
- Ligands: PO4.28
5 PLIP interactions:5 interactions with chain J- Hydrophobic interactions: J:L.61, J:K.97, J:V.122, J:K.165
- Hydrogen bonds: J:D.40
KIK.33: 9 residues within 4Å:- Chain K: D.40, L.61, K.97, S.120, V.122, R.163, K.165, F.249
- Ligands: PO4.31
6 PLIP interactions:6 interactions with chain K- Hydrophobic interactions: K:L.61, K:K.97, K:V.122, K:K.165
- Hydrogen bonds: K:D.40, K:K.97
KIK.36: 9 residues within 4Å:- Chain L: D.40, L.61, K.97, S.120, V.122, R.163, K.165, F.249
- Ligands: PO4.34
6 PLIP interactions:6 interactions with chain L- Hydrophobic interactions: L:L.61, L:K.97, L:V.122, L:K.165
- Hydrogen bonds: L:D.40, L:K.97
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Rodrigues, M.J. et al., Lysine relay mechanism coordinates intermediate transfer in vitamin B6 biosynthesis. Nat. Chem. Biol. (2017)
- Release Date
- 2017-01-18
- Peptides
- Pyridoxal 5'-phosphate synthase subunit PDX1.3: ABCDEFGHIJKL
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
AF
BG
CH
DI
AJ
BK
CL
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.73 Å
- Oligo State
- homo-12-mer
- Ligands
- 12 x PO4: PHOSPHATE ION(Non-functional Binders)
- 12 x SO4: SULFATE ION(Non-functional Binders)
- 12 x KIK: (4~{S})-4-azanyl-5-oxidanyl-pent-1-en-3-one(Covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Rodrigues, M.J. et al., Lysine relay mechanism coordinates intermediate transfer in vitamin B6 biosynthesis. Nat. Chem. Biol. (2017)
- Release Date
- 2017-01-18
- Peptides
- Pyridoxal 5'-phosphate synthase subunit PDX1.3: ABCDEFGHIJKL
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
AF
BG
CH
DI
AJ
BK
CL
D