Research workbench
Crystal structure of TTHA0275 from thermus thermophilus (HB8) in complex with 5'-methylthioadenosine in space group P21212
Analyse Crystal structure of TTHA0275 from thermus thermophilus (HB8) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4X3L
- 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
- MTA, CL
- Pockets
- 8 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | RNA 2'-O ribose methyltransferase | protein | 260 | 37% helix, 20% strand | Q5SLL8 |
Ligands and binding sites
- MTA · 5'-deoxy-5'-methylthioadenosine · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 125 | 0.62 | 0.86 | 22 | MTA |
| 2 | 131 | 0.61 | 0.85 | 22 | MTA |
| 3 | 380 | 0.59 | 0.76 | 39 | empty |
| 4 | 162 | 0.53 | 0.79 | 23 | empty |
| 5 | 96 | 0.46 | 0.80 | 20 | CL |
Interfaces
1 interface between chains.
- A–B · 1435 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4X3L · Crystal Structure of TTHA0275 from Thermus thermophilus (HB8) in complex with… · 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 4X3L · PDBe 4X3L · UniProt Q5SLL8
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