Research workbench
Crystal structure of probable rRNA-methyltransferase from porphyromonas gingivalis
Analyse Crystal structure of probable rRNA-methyltransferase from porphyromonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KW2
- Type
- protein
- Length
- 478 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable R-RNA methyltransferase
- UniProt
- B2RH75
- Ligands
- ADN
- Pockets
- 10 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable R-RNA methyltransferase | protein | 240 | 32% helix, 26% strand | B2RH75 |
| B | Probable R-RNA methyltransferase | protein | 238 | 32% helix, 26% strand | B2RH75 |
Ligands and binding sites
- ADN · Adenosine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 288 | 0.72 | 0.85 | 43 | ADN |
| 2 | 200 | 0.65 | 0.85 | 33 | ADN |
| 3 | 55 | 0.57 | 0.90 | 20 | empty |
| 4 | 81 | 0.38 | 0.77 | 17 | empty |
| 5 | 109 | 0.37 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1487 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 3KW2 · Crystal structure of probable rRNA-methyltransferase from Porphyromonas gingivalis · 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 B2RH75
- Elsewhere: RCSB PDB 3KW2 · PDBe 3KW2 · UniProt B2RH75
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