MolNFT v1 · #56541 · protein
Crystal structure of TTHA0409, putative DNA modification methylase from thermus thermophilus HB8- complexed with S-adenosyl-L-methionine
2ZIF · Putative modification methylase: “Crystal structure of TTHA0409, putative DNA modification methylase from thermus thermophilus HB8- complexed…”. X-ray diffraction, 1 ligand (SAM), 7 pockets (best druggability 0.59). MolNFT v1 #56541…
- PDB
- 2ZIF
- Type
- protein
- Length
- 482 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative modification methylase
- UniProt
- Q5SL84
- Ligands
- SAM
- Pockets
- 7 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative modification methylase | protein | 239 | 36% helix, 23% strand | Q5SL84 |
| B | Putative modification methylase | protein | 243 | 35% helix, 23% strand | Q5SL84 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 384 | 0.59 | 0.76 | 47 | SAM |
| 2 | 199 | 0.57 | 0.80 | 27 | empty |
| 3 | 175 | 0.54 | 0.79 | 27 | empty |
| 4 | 113 | 0.51 | 0.81 | 20 | empty |
| 5 | 174 | 0.49 | 0.77 | 30 | SAM |
Interfaces
1 interface between chains.
- A–B · 2564 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 2ZIF · Crystal Structure of TTHA0409, Putative DNA Modification Methylase from Thermus… · the same entry in another collection · chain B against B, 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 Q5SL84
- Elsewhere: RCSB PDB 2ZIF · PDBe 2ZIF · UniProt Q5SL84
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