MolNFT v1 · #113202 · protein
Crystal structure of the riboflavin kinase module of FAD synthetase from corynebacterium ammoniagenes in complex with ADP
5A88 · Riboflavin biosynthesis protein ribf: “Crystal structure of the riboflavin kinase module of FAD synthetase from corynebacterium ammoniagenes in…”. X-ray diffraction, 2 ligands (ADP, CA), 10 pockets (best druggability 0.67). MolNFT…
- 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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