- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.20 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x N46: (2R)-2-hydroxy-3,4-dioxopentyl dihydrogen phosphate(Non-covalent)
- 2 x 5RP: RIBULOSE-5-PHOSPHATE(Non-covalent)
5RP.2: 18 residues within 4Å:- Chain A: R.38, E.39, D.43, I.66, C.68, N.92, T.94, F.96, L.141, R.151, G.153, H.154, T.155, L.173, E.175
- Chain B: H.137
- Ligands: N46.1, MN.3
10 PLIP interactions:1 interactions with chain B, 9 interactions with chain A- Water bridges: B:H.137, A:E.39, A:E.41, A:R.151
- Hydrogen bonds: A:T.94, A:H.154, A:T.155, A:T.155
- Salt bridges: A:R.38, A:R.151
5RP.9: 18 residues within 4Å:- Chain A: H.137
- Chain B: R.38, E.39, D.43, I.66, C.68, N.92, T.94, F.96, L.141, R.151, G.153, H.154, T.155, L.173, E.175
- Ligands: N46.8, MN.10
10 PLIP interactions:9 interactions with chain B, 1 interactions with chain A- Hydrogen bonds: B:T.94, B:H.154, B:T.155, B:T.155, B:E.175
- Water bridges: B:E.39, B:R.151, A:H.137
- Salt bridges: B:R.38, B:R.151
- 4 x MN: MANGANESE (II) ION(Non-covalent)
MN.3: 6 residues within 4Å:- Chain A: R.38, E.39, D.43, H.154
- Ligands: N46.1, 5RP.2
3 PLIP interactions:2 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:E.39, A:H.154, H2O.1
MN.4: 6 residues within 4Å:- Chain A: Q.75, A.123, P.125, Q.168, P.169, A.170
No protein-ligand interaction detected (PLIP)MN.10: 6 residues within 4Å:- Chain B: R.38, E.39, D.43, H.154
- Ligands: N46.8, 5RP.9
3 PLIP interactions:2 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:E.39, B:H.154, H2O.3
MN.11: 6 residues within 4Å:- Chain B: Q.75, A.123, P.125, Q.168, P.169, A.170
No protein-ligand interaction detected (PLIP)- 6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.5: 6 residues within 4Å:- Chain A: R.38, E.39, A.91, N.92
- Chain B: T.107, T.108
3 PLIP interactions:2 interactions with chain A, 1 interactions with chain B- Hydrogen bonds: A:N.92, A:N.92, B:T.107
EDO.6: 9 residues within 4Å:- Chain A: I.60, R.61, E.62, C.63, T.177, N.178, P.179
- Chain B: I.60, R.61
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:C.63
EDO.7: 7 residues within 4Å:- Chain A: Y.46, T.52, A.54, Q.55, L.58, H.196, M.198
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:H.196
- Water bridges: A:T.52, A:Q.55, A:Q.55
EDO.12: 6 residues within 4Å:- Chain A: T.107, T.108
- Chain B: R.38, E.39, A.91, N.92
3 PLIP interactions:2 interactions with chain B, 1 interactions with chain A- Hydrogen bonds: B:N.92, B:N.92, A:T.107
EDO.13: 9 residues within 4Å:- Chain A: I.60, R.61
- Chain B: I.60, R.61, E.62, C.63, T.177, N.178, P.179
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:C.63
EDO.14: 7 residues within 4Å:- Chain B: Y.46, T.52, A.54, Q.55, L.58, H.196, M.198
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:H.196
- Water bridges: B:T.52, B:Q.55, B:Q.55
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Kenjic, N. et al., Evidence for the Chemical Mechanism of RibB (3,4-Dihydroxy-2-butanone 4-phosphate Synthase) of Riboflavin Biosynthesis. J.Am.Chem.Soc. (2022)
- Release Date
- 2022-07-20
- Peptides
- 3,4-dihydroxy-2-butanone 4-phosphate synthase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.20 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x N46: (2R)-2-hydroxy-3,4-dioxopentyl dihydrogen phosphate(Non-covalent)
- 2 x 5RP: RIBULOSE-5-PHOSPHATE(Non-covalent)
- 4 x MN: MANGANESE (II) ION(Non-covalent)
- 6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Kenjic, N. et al., Evidence for the Chemical Mechanism of RibB (3,4-Dihydroxy-2-butanone 4-phosphate Synthase) of Riboflavin Biosynthesis. J.Am.Chem.Soc. (2022)
- Release Date
- 2022-07-20
- Peptides
- 3,4-dihydroxy-2-butanone 4-phosphate synthase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
A