Research workbench
Crystal structure of the riboflavin kinase module of FAD synthetase from corynebacterium ammoniagenes in complex with ADP
Analyse Crystal structure of the riboflavin kinase module of FAD synthetase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5A88
- Type
- protein
- Length
- 555 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Riboflavin biosynthesis protein ribf
- EC
- 2.7.1.26, 2.7.7.2
- UniProt
- Q59263
- Ligands
- ADP, CA
- Pockets
- 10 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 19% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Riboflavin biosynthesis protein ribf (EC 2.7.1.26, 2.7.7.2) | protein | 147 | 20% helix, 38% strand | Q59263 |
| B | Riboflavin biosynthesis protein ribf (EC 2.7.1.26, 2.7.7.2) | protein | 133 | 17% helix, 40% strand | Q59263 |
| C | Riboflavin biosynthesis protein ribf (EC 2.7.1.26, 2.7.7.2) | protein | 138 | 18% helix, 40% strand | Q59263 |
| D | Riboflavin biosynthesis protein ribf (EC 2.7.1.26, 2.7.7.2) | protein | 137 | 18% helix, 39% strand | Q59263 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 6 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 375 | 0.67 | 0.80 | 46 | ADP, GOL, CA |
| 2 | 379 | 0.64 | 0.78 | 47 | ADP, GOL, CA |
| 3 | 183 | 0.53 | 0.78 | 24 | empty |
| 4 | 300 | 0.52 | 0.74 | 42 | GOL |
| 5 | 154 | 0.50 | 0.78 | 24 | empty |
Interfaces
4 interfaces between chains.
- B–D · 576 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 521 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 463 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 133 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5A88 · Crystal structure of the riboflavin kinase module of FAD synthetase from Corynebacterium… · the same entry in another collection · chain D against D, TM-score 1.00
- Q59263 · AlphaFold monomer V2.0 prediction for bifunctional riboflavin KINASE/FMN… · a predicted model of the same protein · chain B against A, TM-score 0.93
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 Q59263
- Elsewhere: RCSB PDB 5A88 · PDBe 5A88 · UniProt Q59263
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