MolNFT v1 · #147416 · protein
VLM2 thioesterase domain with genetically encoded 2,3-diaminopropionic acid bound with a dodecadepsipeptide, space group H3
6ECE: “VLM2 thioesterase domain with genetically encoded 2,3-diaminopropionic acid bound with a dodecadepsipeptide…”. X-ray diffraction, 2 ligands (DVA, 2OP), 5 pockets (best druggability 0.75). MolNFT v1 #147416 on GenesisL1: 3D…
- PDB
- 6ECE
- Type
- protein
- Length
- 494 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VLM2; Dodecadepsipeptide
- EC
- 3.1.2.-
- UniProt
- Q1PSF3
- Ligands
- DVA, 2OP
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VLM2 (EC 3.1.2.-) | protein | 255 | 46% helix, 16% strand | Q1PSF3 |
| B | VLM2 (EC 3.1.2.-) | protein | 237 | 46% helix, 15% strand | Q1PSF3 |
| C, D | Dodecadepsipeptide | protein | 1 | 0% helix, 0% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 776 | 0.75 | 0.79 | 49 | DVA, 2OP |
| 2 | 577 | 0.65 | 0.75 | 43 | empty |
| 3 | 129 | 0.51 | 0.80 | 26 | empty |
| 4 | 85 | 0.41 | 0.78 | 20 | empty |
| 5 | 99 | 0.38 | 0.75 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 654 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 167 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 163 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified, 1 covalent (nonstandard, covalent ligand).
Compared structures
- 6ECE · 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 6ECE · PDBe 6ECE · UniProt Q1PSF3
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