MolNFT v1 · #77153 · protein
Crystal structure of a putative glycosidase (BT_4094) from bacteroides thetaiotaomicron vpi-5482 at 2.30 a resolution
3R67: “Crystal structure of a putative glycosidase (BT_4094) from bacteroides thetaiotaomicron vpi-5482 at 2.30 a…”. X-ray diffraction, 17 pockets (best druggability 0.62). MolNFT v1 #77153 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3R67
- Type
- protein
- Length
- 1,395 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative glycosidase
- UniProt
- Q8A0C7
- Pockets
- 17 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Putative glycosidase | protein | 349 | 3% helix, 44% strand | Q8A0C7 |
| D | Putative glycosidase | protein | 348 | 4% helix, 44% strand | Q8A0C7 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 20 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 444 | 0.62 | 0.76 | 34 | EDO |
| 2 | 146 | 0.54 | 0.81 | 23 | EDO |
| 3 | 158 | 0.53 | 0.79 | 23 | EDO |
| 4 | 203 | 0.52 | 0.77 | 32 | empty |
| 5 | 246 | 0.52 | 0.76 | 31 | empty |
Interfaces
5 interfaces between chains.
- A–B · 349 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 263 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 260 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 252 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 173 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 3R67 · Crystal structure of a putative glycosidase (BT_4094) from BACTEROIDES THETAIOTAOMICRON… · 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 Q8A0C7
- Elsewhere: RCSB PDB 3R67 · PDBe 3R67 · UniProt Q8A0C7
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