Research workbench
The crystal structure of ribd from escherichia COLI in complex with the oxidised NADP+ cofactor in the active site of the reductase domain
Analyse The crystal structure of ribd from escherichia COLI in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2O7P
- Type
- protein
- Length
- 711 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Riboflavin biosynthesis protein ribd
- EC
- 3.5.4.26, 1.1.1.193
- UniProt
- P25539
- Ligands
- NAP
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Riboflavin biosynthesis protein ribd (EC 3.5.4.26, 1.1.1.193) | protein | 358 | 32% helix, 24% strand | P25539 |
| B | Riboflavin biosynthesis protein ribd (EC 3.5.4.26, 1.1.1.193) | protein | 353 | 31% helix, 23% strand | P25539 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 325 | 0.72 | 0.85 | 53 | empty |
| 2 | 336 | 0.65 | 0.80 | 40 | empty |
| 3 | 219 | 0.64 | 0.83 | 32 | empty |
| 4 | 281 | 0.63 | 0.80 | 38 | NAP |
| 5 | 112 | 0.49 | 0.80 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1279 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 modified (engineered).
Compared structures
- 2O7P · The crystal structure of RibD from Escherichia coli in complex with the oxidised NADP+… · the same entry in another collection · chain A against A, TM-score 1.00
- P25539 · AlphaFold monomer V2.0 prediction for riboflavin biosynthesis protein ribd (P25539) · a predicted model of the same protein · chain A against A, TM-score 0.95
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P25539
- Elsewhere: RCSB PDB 2O7P · PDBe 2O7P · UniProt P25539
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