Research workbench
Crystal structure of complex of SAM and BVU_3255, a methyltransferase from bacteroides vulgatus atcc 8482
Analyse Crystal structure of complex of SAM and BVU_3255, a methyltransferase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3T7S
- Type
- protein
- Length
- 965 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative methyltransferase
- UniProt
- A6L5C0
- Ligands
- SAM
- Pockets
- 11 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative methyltransferase | protein | 246 | 44% helix, 23% strand | A6L5C0 |
| B | Putative methyltransferase | protein | 239 | 41% helix, 24% strand | A6L5C0 |
| C | Putative methyltransferase | protein | 245 | 43% helix, 24% strand | A6L5C0 |
| D | Putative methyltransferase | protein | 235 | 40% helix, 25% strand | A6L5C0 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 715 | 0.72 | 0.78 | 82 | empty |
| 2 | 870 | 0.71 | 0.77 | 58 | empty |
| 3 | 408 | 0.67 | 0.79 | 44 | SAM |
| 4 | 366 | 0.66 | 0.80 | 44 | SAM |
| 5 | 307 | 0.64 | 0.80 | 45 | SAM |
Interfaces
5 interfaces between chains.
- C–D · 973 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 841 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 228 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 201 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 119 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3T7S · Crystal structure of complex of SAM and BVU_3255, a methyltransferase from Bacteroides… · 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 A6L5C0
- Elsewhere: RCSB PDB 3T7S · PDBe 3T7S · UniProt A6L5C0
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