MolNFT v1 · #60570 · protein
Crystal structure of a methyltransferase-like protein (SPO2022) from silicibacter pomeroyi dss-3 at 1.80 a resolution
3CVO · Methyltransferase-like protein of unknown function: “Crystal structure of a methyltransferase-like protein (SPO2022) from silicibacter pomeroyi dss-3 at 1.80 a…”. X-ray diffraction, 1 ligand (SO4), 8 pockets (best druggability…
- PDB
- 3CVO
- Type
- protein
- Length
- 776 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methyltransferase-like protein of unknown function
- UniProt
- Q5LRV1
- Ligands
- SO4
- Pockets
- 8 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Methyltransferase-like protein of unknown function | protein | 194 | 41% helix, 19% strand | Q5LRV1 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 46 copies · chains A, D, B, C
- GOL · Glycerol · additive
- PG4 · Tetraethylene glycol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 307 | 0.58 | 0.77 | 40 | EDO |
| 2 | 168 | 0.53 | 0.79 | 25 | empty |
| 3 | 194 | 0.52 | 0.78 | 26 | empty |
| 4 | 176 | 0.50 | 0.77 | 23 | empty |
| 5 | 165 | 0.48 | 0.77 | 22 | EDO |
Interfaces
4 interfaces between chains.
- C–D · 1060 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 1023 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 238 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 195 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified (engineered).
Compared structures
- 3CVO · Crystal structure of a methyltransferase-like protein (spo2022) from silicibacter… · 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 Q5LRV1
- Elsewhere: RCSB PDB 3CVO · PDBe 3CVO · UniProt Q5LRV1
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