MolNFT v1 · #80084 · protein
BD1817, a HDG"Y"P protein from bdellovibrio bacteriovorus
3TM8 · Uncharacterized protein: “BD1817, a HDG"Y"P protein from bdellovibrio bacteriovorus”. X-ray diffraction, 2 ligands (FE, PO4), 14 pockets (best druggability 0.76). MolNFT v1 #80084 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3TM8
- Type
- protein
- Length
- 616 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- Q6MM30
- Ligands
- FE, PO4
- Pockets
- 14 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 60% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein | protein | 309 | 60% helix, 8% strand | Q6MM30 |
| B | Uncharacterized protein | protein | 307 | 60% 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
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 285 | 0.76 | 0.89 | 44 | DMS |
| 2 | 724 | 0.72 | 0.78 | 67 | empty |
| 3 | 68 | 0.70 | 0.97 | 21 | EDO |
| 4 | 419 | 0.69 | 0.81 | 51 | empty |
| 5 | 139 | 0.56 | 0.82 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 918 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3TM8 · 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 3TM8 · PDBe 3TM8 · UniProt Q6MM30
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