Research workbench
BD1817, a HDG"Y"P protein from bdellovibrio bacteriovorus
Analyse BD1817, a HDG"Y"P protein from bdellovibrio bacteriovorus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TMB
- Type
- protein
- Length
- 625 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein BD1817
- UniProt
- Q6MM30
- Ligands
- FE, PO4
- Pockets
- 10 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 58% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein BD1817 | protein | 307 | 59% helix, 8% strand | Q6MM30 |
| B | Uncharacterized protein BD1817 | protein | 318 | 57% helix, 8% strand | Q6MM30 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 4 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 61 | 0.70 | 0.97 | 19 | empty |
| 2 | 142 | 0.55 | 0.82 | 25 | empty |
| 3 | 149 | 0.54 | 0.81 | 22 | empty |
| 4 | 185 | 0.51 | 0.77 | 27 | empty |
| 5 | 151 | 0.50 | 0.78 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 217 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3TMB · Bd1817, a HDGY"P protein from Bdellovibrio bacteriovorus" · 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 Q6MM30
- Elsewhere: RCSB PDB 3TMB · PDBe 3TMB · UniProt Q6MM30
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.