MolNFT v1 · #151050 · protein
Bdellovibrio bacteriovorus dgcb full-length
6HBZ · Ggdef domain protein: “Bdellovibrio bacteriovorus dgcb full-length”. X-ray diffraction, 2 ligands (C2E, CL), 1 pocket (best druggability 0.76). MolNFT v1 #151050 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6HBZ
- Type
- protein
- Length
- 539 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ggdef domain protein
- UniProt
- Q6MPU8
- Ligands
- C2E, CL
- Pockets
- 1 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ggdef domain protein | protein | 269 | 31% helix, 30% strand | Q6MPU8 |
| B | Ggdef domain protein | protein | 270 | 29% helix, 30% strand | Q6MPU8 |
Ligands and binding sites
- C2E · 9,9'-[(2r,3r,3as,5s,7ar,9r,10r,10as,12s,14ar)-3,5,10, 12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3, 2-D:3',2'-J][1,3,7,9,2, 8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1008 | 0.76 | 0.79 | 98 | C2E |
Interfaces
1 interface between chains.
- A–B · 1242 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 6HBZ · Bdellovibrio bacteriovorus DgcB Full-length · 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 Q6MPU8
- Elsewhere: RCSB PDB 6HBZ · PDBe 6HBZ · UniProt Q6MPU8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.