MolNFT v1 · #51584 · protein
Riboflavin kinase MJ0056 from methanocaldococcus jannaschii in complex with cdp and PO4
2VBT: “Riboflavin kinase MJ0056 from methanocaldococcus jannaschii in complex with cdp and PO4”. X-ray diffraction, 3 ligands (CDP, NA, PO4), 2 pockets (best druggability 0.59). MolNFT v1 #51584 on GenesisL1: 3D structure, binding sites…
- PDB
- 2VBT
- Type
- protein
- Length
- 136 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Riboflavin kinase
- EC
- 2.7.1.161
- UniProt
- Q60365
- Ligands
- CDP, NA, PO4
- Pockets
- 2 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 18% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Riboflavin kinase (EC 2.7.1.161) | protein | 136 | 18% helix, 39% strand | Q60365 |
Ligands and binding sites
- CDP · Cytidine-5'-diphosphate · ligand · chains A
- NA · Sodium ion · metal · chains A
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 249 | 0.59 | 0.79 | 36 | CDP, NA, PO4 |
| 2 | 58 | 0.38 | 0.80 | 16 | empty |
Compared structures
- 2VBT · Riboflavin kinase Mj0056 from Methanocaldococcus jannaschii in complex with CDP and PO4 · 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 A 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 2VBT · PDBe 2VBT · UniProt Q60365
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