Research workbench
Crystal structure of a bifunctional deaminase and reductase involved in riboflavin biosynthesis
Analyse Crystal structure of a bifunctional deaminase and reductase involved in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2D5N
- Type
- protein
- Length
- 1,437 residues
- Chains
- 4
- 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
- P17618
- Ligands
- NDP, ZN
- Pockets
- 15 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Riboflavin biosynthesis protein ribd (EC 3.5.4.26, 1.1.1.193) | protein | 359 | 30% helix, 22% strand | P17618 |
| D | Riboflavin biosynthesis protein ribd (EC 3.5.4.26, 1.1.1.193) | protein | 360 | 30% helix, 24% strand | P17618 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · chains B
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 573 | 0.72 | 0.80 | 53 | empty |
| 2 | 568 | 0.71 | 0.80 | 54 | empty |
| 3 | 554 | 0.70 | 0.79 | 54 | empty |
| 4 | 534 | 0.69 | 0.79 | 49 | NDP |
| 5 | 480 | 0.68 | 0.79 | 54 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2066 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 2042 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1159 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 1011 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2D5N · Crystal structure of a bifunctional deaminase and reductase involved in riboflavin… · the same entry in another collection · chain A against A, TM-score 1.00
- P17618 · AlphaFold monomer V2.0 prediction for riboflavin biosynthesis protein ribd (P17618) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P17618
- Elsewhere: RCSB PDB 2D5N · PDBe 2D5N · UniProt P17618
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