Research workbench
Crystal structure of TTHA0275 from thermus thermophilus (HB8) in complex with adenosine in space group P212121
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
- 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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