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
- 3TMD
- Type
- protein
- Length
- 305 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- UniProt
- Q6MM30
- Ligands
- FE, PO4
- Pockets
- 5 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 58% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein | protein | 305 | 58% helix, 7% strand | Q6MM30 |
Ligands and binding sites
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 | 165 | 0.57 | 0.81 | 24 | empty |
| 2 | 116 | 0.41 | 0.75 | 19 | empty |
| 3 | 54 | 0.40 | 0.81 | 13 | empty |
| 4 | 76 | 0.37 | 0.77 | 17 | empty |
| 5 | 50 | 0.32 | 0.77 | 10 | empty |
Compared structures
- 3TMD · 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 3TMD · PDBe 3TMD · UniProt Q6MM30
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