MolNFT v1 · #156601 · protein
Bbvci B2 dimer with TA6BR14 clusters
6M9G · Bbvci endonuclease subunit 2: “Bbvci B2 dimer with TA6BR14 clusters”. X-ray diffraction, 3 ligands (TBR, BR, SO4), 5 pockets (best druggability 0.62). MolNFT v1 #156601 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6M9G
- Type
- protein
- Length
- 546 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bbvci endonuclease subunit 2
- UniProt
- Q5D6Y4
- Ligands
- TBR, BR, SO4
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bbvci endonuclease subunit 2 | protein | 280 | 45% helix, 25% strand | Q5D6Y4 |
| B | Bbvci endonuclease subunit 2 | protein | 266 | 43% helix, 27% strand | Q5D6Y4 |
Ligands and binding sites
- TBR · Hexatantalum dodecabromide · ligand · 10 copies · chains A, B
- BR · Bromide ion · ion · 6 copies · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
- ACT · Acetate ion · additive · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 452 | 0.62 | 0.76 | 57 | TBR |
| 2 | 96 | 0.34 | 0.74 | 17 | empty |
| 3 | 63 | 0.33 | 0.76 | 12 | empty |
| 4 | 72 | 0.32 | 0.74 | 17 | empty |
| 5 | 87 | 0.32 | 0.72 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 770 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6M9G · BbvCI B2 dimer with Ta6Br14 clusters · the same entry in another collection · chain A against A, 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 Q5D6Y4
- Elsewhere: RCSB PDB 6M9G · PDBe 6M9G · UniProt Q5D6Y4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.