- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.23 Å
- Oligo State
- homo-12-mer
- Ligands
- 12 x PO4: PHOSPHATE ION(Non-functional Binders)
- 12 x KPR: [(~{E},4~{S})-4-azanyl-3-oxidanylidene-pent-1-enyl] dihydrogen phosphate(Covalent)
KPR.2: 16 residues within 4Å:- Chain A: D.40, M.59, P.65, K.97, D.118, S.120, R.163, A.168, G.169, A.228, G.229, G.230, F.249, V.250, G.251, S.252
11 PLIP interactions:11 interactions with chain A- Hydrophobic interactions: A:K.97
- Hydrogen bonds: A:D.40, A:G.169, A:G.229, A:G.230, A:G.251, A:S.252, A:S.252
- Water bridges: A:V.231, A:S.252, A:G.253
KPR.4: 16 residues within 4Å:- Chain B: D.40, M.59, P.65, K.97, D.118, S.120, R.163, A.168, G.169, A.228, G.229, G.230, F.249, V.250, G.251, S.252
12 PLIP interactions:12 interactions with chain B- Hydrophobic interactions: B:K.97
- Hydrogen bonds: B:D.40, B:G.169, B:G.229, B:G.230, B:G.251, B:S.252, B:S.252
- Water bridges: B:T.170, B:V.231, B:V.231, B:G.253
KPR.6: 16 residues within 4Å:- Chain C: D.40, M.59, P.65, K.97, D.118, S.120, R.163, A.168, G.169, A.228, G.229, G.230, F.249, V.250, G.251, S.252
10 PLIP interactions:10 interactions with chain C- Hydrophobic interactions: C:P.65, C:K.97
- Hydrogen bonds: C:D.40, C:G.169, C:G.229, C:G.230, C:G.251, C:S.252
- Water bridges: C:V.231, C:V.231
KPR.8: 16 residues within 4Å:- Chain D: D.40, M.59, P.65, K.97, D.118, S.120, R.163, A.168, G.169, A.228, G.229, G.230, F.249, V.250, G.251, S.252
11 PLIP interactions:11 interactions with chain D- Hydrophobic interactions: D:P.65, D:K.97
- Hydrogen bonds: D:D.40, D:G.169, D:G.229, D:G.230, D:G.251, D:S.252
- Water bridges: D:V.231, D:G.253, D:G.253
KPR.10: 16 residues within 4Å:- Chain E: D.40, M.59, P.65, K.97, D.118, S.120, R.163, A.168, G.169, A.228, G.229, G.230, F.249, V.250, G.251, S.252
11 PLIP interactions:11 interactions with chain E- Hydrophobic interactions: E:K.97
- Hydrogen bonds: E:D.40, E:G.169, E:G.229, E:G.230, E:G.251, E:S.252, E:S.252
- Water bridges: E:V.231, E:S.252, E:G.253
KPR.12: 16 residues within 4Å:- Chain F: D.40, M.59, P.65, K.97, D.118, S.120, R.163, A.168, G.169, A.228, G.229, G.230, F.249, V.250, G.251, S.252
12 PLIP interactions:12 interactions with chain F- Hydrophobic interactions: F:K.97
- Hydrogen bonds: F:D.40, F:G.169, F:G.229, F:G.230, F:G.251, F:S.252, F:S.252
- Water bridges: F:T.170, F:V.231, F:V.231, F:G.253
KPR.14: 16 residues within 4Å:- Chain G: D.40, M.59, P.65, K.97, D.118, S.120, R.163, A.168, G.169, A.228, G.229, G.230, F.249, V.250, G.251, S.252
10 PLIP interactions:10 interactions with chain G- Hydrophobic interactions: G:P.65, G:K.97
- Hydrogen bonds: G:D.40, G:G.169, G:G.229, G:G.230, G:G.251, G:S.252
- Water bridges: G:V.231, G:V.231
KPR.16: 16 residues within 4Å:- Chain H: D.40, M.59, P.65, K.97, D.118, S.120, R.163, A.168, G.169, A.228, G.229, G.230, F.249, V.250, G.251, S.252
11 PLIP interactions:11 interactions with chain H- Hydrophobic interactions: H:P.65, H:K.97
- Hydrogen bonds: H:D.40, H:G.169, H:G.229, H:G.230, H:G.251, H:S.252
- Water bridges: H:V.231, H:G.253, H:G.253
KPR.18: 16 residues within 4Å:- Chain I: D.40, M.59, P.65, K.97, D.118, S.120, R.163, A.168, G.169, A.228, G.229, G.230, F.249, V.250, G.251, S.252
11 PLIP interactions:11 interactions with chain I- Hydrophobic interactions: I:K.97
- Hydrogen bonds: I:D.40, I:G.169, I:G.229, I:G.230, I:G.251, I:S.252, I:S.252
- Water bridges: I:V.231, I:S.252, I:G.253
KPR.20: 16 residues within 4Å:- Chain J: D.40, M.59, P.65, K.97, D.118, S.120, R.163, A.168, G.169, A.228, G.229, G.230, F.249, V.250, G.251, S.252
12 PLIP interactions:12 interactions with chain J- Hydrophobic interactions: J:K.97
- Hydrogen bonds: J:D.40, J:G.169, J:G.229, J:G.230, J:G.251, J:S.252, J:S.252
- Water bridges: J:T.170, J:V.231, J:V.231, J:G.253
KPR.22: 16 residues within 4Å:- Chain K: D.40, M.59, P.65, K.97, D.118, S.120, R.163, A.168, G.169, A.228, G.229, G.230, F.249, V.250, G.251, S.252
10 PLIP interactions:10 interactions with chain K- Hydrophobic interactions: K:P.65, K:K.97
- Hydrogen bonds: K:D.40, K:G.169, K:G.229, K:G.230, K:G.251, K:S.252
- Water bridges: K:V.231, K:V.231
KPR.24: 16 residues within 4Å:- Chain L: D.40, M.59, P.65, K.97, D.118, S.120, R.163, A.168, G.169, A.228, G.229, G.230, F.249, V.250, G.251, S.252
11 PLIP interactions:11 interactions with chain L- Hydrophobic interactions: L:P.65, L:K.97
- Hydrogen bonds: L:D.40, L:G.169, L:G.229, L:G.230, L:G.251, L:S.252
- Water bridges: L:V.231, L:G.253, L:G.253
- 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
AB
BC
CD
DE
AF
BG
CH
DI
AJ
BK
CL
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.23 Å
- Oligo State
- homo-12-mer
- Ligands
- 12 x PO4: PHOSPHATE ION(Non-functional Binders)
- 12 x KPR: [(~{E},4~{S})-4-azanyl-3-oxidanylidene-pent-1-enyl] dihydrogen phosphate(Covalent)
- 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
AB
BC
CD
DE
AF
BG
CH
DI
AJ
BK
CL
D