MolNFT v1 · #175895 · protein
Crystal structure of a truly knotted protein: cyclized yibk from haemophilus influenzae
7D51 · TRNA (CYTIDINE(34)-2'-O)-methyltransferase: “Crystal structure of a truly knotted protein: cyclized yibk from haemophilus influenzae”. X-ray diffraction, 3 pockets (best druggability 0.60). MolNFT v1 #175895 on GenesisL1: 3D…
- PDB
- 7D51
- Type
- protein
- Length
- 327 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA (CYTIDINE(34)-2'-O)-methyltransferase
- EC
- 2.1.1.207
- UniProt
- P44868
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TRNA (CYTIDINE(34)-2'-O)-methyltransferase (EC 2.1.1.207) | protein | 161 | 29% helix, 17% strand | P44868 |
| B | TRNA (CYTIDINE(34)-2'-O)-methyltransferase (EC 2.1.1.207) | protein | 166 | 32% helix, 16% strand | P44868 |
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 294 | 0.60 | 0.78 | 38 | empty |
| 2 | 257 | 0.59 | 0.79 | 34 | empty |
| 3 | 101 | 0.40 | 0.76 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1786 Ų buried · 44 hydrogen bonds · protein-protein
Compared structures
- 7D51 · Crystal structure of a truly knotted protein: cyclized YibK from Haemophilus influenzae · the same entry in another collection · chain A against A, TM-score 1.00
- P44868 · AlphaFold monomer V2.0 prediction for tRNA (CYTIDINE(34)-2'-O)-methyltransferase (P44868) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P44868
- Elsewhere: RCSB PDB 7D51 · PDBe 7D51 · UniProt P44868
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