Research workbench
Crystal structure of TT0168 from thermus thermophilus HB8
Analyse Crystal structure of TT0168 from thermus thermophilus HB8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1V25
- Type
- protein
- Length
- 998 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Long-chain-fatty-acid-CoA synthetase
- EC
- 6.2.1.3
- UniProt
- Q6L8F0
- Ligands
- ANP, MG
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Long-chain-fatty-acid-CoA synthetase (EC 6.2.1.3) | protein | 491 | 31% helix, 25% strand | Q6L8F0 |
| B | Long-chain-fatty-acid-CoA synthetase (EC 6.2.1.3) | protein | 507 | 33% helix, 24% strand | Q6L8F0 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 796 | 0.81 | 0.84 | 97 | MG, ANP |
| 2 | 770 | 0.80 | 0.84 | 96 | MG, ANP |
| 3 | 210 | 0.64 | 0.83 | 31 | empty |
| 4 | 223 | 0.64 | 0.82 | 34 | empty |
| 5 | 102 | 0.48 | 0.80 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 2939 Ų buried · 43 hydrogen bonds · protein-protein
Compared structures
- 1V25 · Crystal structure of tt0168 from Thermus thermophilus HB8 · 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 Q6L8F0
- Elsewhere: RCSB PDB 1V25 · PDBe 1V25 · UniProt Q6L8F0
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