MolNFT v1 · #25381 · protein
Crystal structure of a degv lipid binding protein (TM1468) from thermotoga maritima at 2.45 a resolution
1VPV · UPF0230 protein TM1468: “Crystal structure of a degv lipid binding protein (TM1468) from thermotoga maritima at 2.45 a resolution”. X-ray diffraction, 2 ligands (PLM, PO4), 5 pockets (best druggability 0.77). MolNFT v1 #25381 on…
- PDB
- 1VPV
- Type
- protein
- Length
- 560 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- UPF0230 protein TM1468
- UniProt
- Q9X1H9
- Ligands
- PLM, PO4
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | UPF0230 protein TM1468 | protein | 282 | 38% helix, 28% strand | Q9X1H9 |
| B | UPF0230 protein TM1468 | protein | 278 | 40% helix, 29% strand | Q9X1H9 |
Ligands and binding sites
- PLM · Palmitic acid · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 132 | 0.77 | 0.95 | 30 | PLM |
| 2 | 127 | 0.77 | 0.95 | 30 | PLM |
| 3 | 767 | 0.77 | 0.81 | 64 | PO4 |
| 4 | 145 | 0.52 | 0.80 | 24 | empty |
| 5 | 119 | 0.47 | 0.79 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 749 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 1VPV · Crystal structure of a degv lipid binding protein (tm1468) from thermotoga maritima at… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9X1H9 · AlphaFold monomer V2.0 prediction for fatty acid-binding protein TM_1468 (Q9X1H9) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9X1H9
- Elsewhere: RCSB PDB 1VPV · PDBe 1VPV · UniProt Q9X1H9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.