Research workbench
Crystal structure of TT1595, a putative SAM-dependent methyltransferase from thermus thermophillus HB8
Analyse Crystal structure of TT1595, a putative SAM-dependent methyltransferase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1WXX
- Type
- protein
- Length
- 1,528 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein TTHA1280
- UniProt
- Q5SIT4
- Ligands
- K, PO4
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Hypothetical protein TTHA1280 | protein | 382 | 35% helix, 32% strand | Q5SIT4 |
Ligands and binding sites
- K · Potassium ion · metal · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 8 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1154 | 0.81 | 0.82 | 109 | empty |
| 2 | 773 | 0.77 | 0.82 | 78 | empty |
| 3 | 1138 | 0.72 | 0.76 | 99 | PO4, K |
| 4 | 777 | 0.69 | 0.76 | 78 | K |
| 5 | 678 | 0.69 | 0.76 | 62 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1359 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1325 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 664 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 387 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 171 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 1WXX · Crystal structure of Tt1595, a putative SAM-dependent methyltransferase from Thermus… · 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 Q5SIT4
- Elsewhere: RCSB PDB 1WXX · PDBe 1WXX · UniProt Q5SIT4
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