Research workbench
X-ray structure of the putative methyltransferase from bacteroides thetaiotaomicron vpi-5482 at the resolution 2.5 a. norteast structural genomics consortium target BTR28
Analyse X-ray structure of the putative methyltransferase from bacteroides… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1WYZ
- Type
- protein
- Length
- 900 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative S-adenosylmethionine-dependent methyltransferase
- UniProt
- Q8A031
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative S-adenosylmethionine-dependent methyltransferase | protein | 223 | 39% helix, 21% strand | Q8A031 |
| B, D | Putative S-adenosylmethionine-dependent methyltransferase | protein | 227 | 37% helix, 20% strand | Q8A031 |
| C | Putative S-adenosylmethionine-dependent methyltransferase | protein | 223 | 37% helix, 22% strand | Q8A031 |
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 572 | 0.77 | 0.84 | 50 | empty |
| 2 | 1170 | 0.77 | 0.79 | 99 | empty |
| 3 | 590 | 0.75 | 0.82 | 66 | empty |
| 4 | 438 | 0.70 | 0.81 | 45 | empty |
| 5 | 153 | 0.46 | 0.76 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2222 Ų buried · 29 hydrogen bonds · protein-protein
- B–D · 2161 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 317 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 1WYZ · X-Ray structure of the putative methyltransferase 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 Q8A031
- Elsewhere: RCSB PDB 1WYZ · PDBe 1WYZ · UniProt Q8A031
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