Research workbench
H. halophila dodecin in complex with riboflavin
Analyse H. halophila dodecin in complex with riboflavin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VXA
- Type
- protein
- Length
- 792 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dodecin
- UniProt
- A1WUH0
- Ligands
- RBF, CL
- Pockets
- 16 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 23% helix, 61% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Dodecin | protein | 66 | 23% helix, 61% strand | A1WUH0 |
Ligands and binding sites
- RBF · Riboflavin · ligand · 12 copies · chains A, C, E, B, K, G, D, F, I, L, H, J
- CL · Chloride ion · ion · 24 copies · chains A, B, C, H, E, F, D, L, G, I, J, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1003 | 0.77 | 0.79 | 85 | RBF, CL |
| 2 | 481 | 0.70 | 0.80 | 40 | CL, RBF |
| 3 | 467 | 0.69 | 0.80 | 35 | RBF, CL |
| 4 | 488 | 0.68 | 0.79 | 39 | RBF, CL |
| 5 | 472 | 0.68 | 0.79 | 41 | CL, RBF |
Interfaces
30 interfaces between chains.
- C–F · 590 Ų buried · 9 hydrogen bonds · protein-protein
- F–G · 581 Ų buried · 9 hydrogen bonds · protein-protein
- D–I · 580 Ų buried · 9 hydrogen bonds · protein-protein
- I–J · 580 Ų buried · 9 hydrogen bonds · protein-protein
- E–L · 580 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2VXA · H. halophila dodecin in complex with riboflavin · the same entry in another collection · chain I against I, TM-score 1.00
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 A1WUH0
- Elsewhere: RCSB PDB 2VXA · PDBe 2VXA · UniProt A1WUH0
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