Research workbench
Riboflavin kinase MJ0056 from methanocaldococcus jannaschii in complex with cdp and FMN
Analyse Riboflavin kinase MJ0056 from methanocaldococcus jannaschii in complex with cdp… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VBV
- Type
- protein
- Length
- 270 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Riboflavin kinase
- EC
- 2.7.1.161
- UniProt
- Q60365
- Ligands
- CDP, FMN, MG, IOD, CL
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Riboflavin kinase (EC 2.7.1.161) | protein | 134 | 19% helix, 40% strand | Q60365 |
| B | Riboflavin kinase (EC 2.7.1.161) | protein | 136 | 17% helix, 38% strand | Q60365 |
Ligands and binding sites
- CDP · Cytidine-5'-diphosphate · ligand · 2 copies · chains A, B
- FMN · Flavin mononucleotide · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A, B
- IOD · Iodide ion · ion · chains A
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 269 | 0.69 | 0.84 | 39 | CDP, FMN |
| 2 | 204 | 0.62 | 0.82 | 25 | empty |
| 3 | 145 | 0.56 | 0.81 | 21 | empty |
| 4 | 114 | 0.52 | 0.82 | 21 | MG, CDP |
| 5 | 78 | 0.39 | 0.78 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 451 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2VBV · Riboflavin kinase Mj0056 from Methanocaldococcus jannaschii in complex with CDP and FMN · the same entry in another collection · chain A against A, TM-score 1.00
- Q60365 · AlphaFold monomer V2.0 prediction for riboflavin kinase (Q60365) · a predicted model of the same protein · chain B against A, TM-score 0.92
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 Q60365
- Elsewhere: RCSB PDB 2VBV · PDBe 2VBV · UniProt Q60365
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