MolNFT v1 · #109469 · protein
Crystal structure of TTHA0275 from thermus thermophilus (HB8) in complex with adenosine in space group P212121
4X3M · RNA 2'-O ribose methyltransferase: “Crystal structure of TTHA0275 from thermus thermophilus (HB8) in complex with adenosine in space group P212121”. X-ray diffraction, 3 ligands (ADN, K, PO4), 4 pockets (best druggability 0.62).…
- PDB
- 4X3M
- Type
- protein
- Length
- 520 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA 2'-O ribose methyltransferase
- UniProt
- Q5SLL8
- Ligands
- ADN, K, PO4
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | RNA 2'-O ribose methyltransferase | protein | 260 | 38% helix, 20% strand | Q5SLL8 |
Ligands and binding sites
- ADN · Adenosine · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · chains B
- PO4 · Phosphate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 347 | 0.62 | 0.78 | 46 | ADN |
| 2 | 146 | 0.60 | 0.84 | 24 | ADN |
| 3 | 116 | 0.45 | 0.78 | 19 | empty |
| 4 | 63 | 0.38 | 0.79 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1557 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 4X3M · Crystal Structure of TTHA0275 from Thermus thermophilus (HB8) in complex with Adenosine… · 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 Q5SLL8
- Elsewhere: RCSB PDB 4X3M · PDBe 4X3M · UniProt Q5SLL8
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