MolNFT v1 · #147415 · protein
VLM2 thioesterase domain with genetically encoded 2,3-diaminopropionic acid bound with a tetradepsipeptide
6ECD: “VLM2 thioesterase domain with genetically encoded 2,3-diaminopropionic acid bound with a tetradepsipeptide”. X-ray diffraction, 1 ligand (2OP), 2 pockets (best druggability 0.65). MolNFT v1 #147415 on GenesisL1: 3D structure…
- PDB
- 6ECD
- Type
- protein
- Length
- 246 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VLM2; Tetradepsipeptide
- EC
- 3.1.2.-
- UniProt
- Q1PSF3
- Ligands
- 2OP
- Pockets
- 2 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VLM2 (EC 3.1.2.-) | protein | 245 | 41% helix, 15% strand | Q1PSF3 |
| B | Tetradepsipeptide | protein | 1 | 0% helix, 0% strand | — |
Ligands and binding sites
- 2OP · (2S)-2-hydroxypropanoic acid · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 234 | 0.65 | 0.83 | 48 | empty |
| 2 | 53 | 0.28 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 150 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, nonstandard).
Compared structures
- 6ECD · Vlm2 thioesterase domain with genetically encoded 2,3-diaminopropionic acid bound with a… · 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 Q1PSF3
- Elsewhere: RCSB PDB 6ECD · PDBe 6ECD · UniProt Q1PSF3
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