MolNFT v1 · #147417 · protein
VLM2 thioesterase domain with genetically encoded 2,3-diaminopropionic acid bound with a dodecadepsipeptide, space group P1
6ECF: “VLM2 thioesterase domain with genetically encoded 2,3-diaminopropionic acid bound with a dodecadepsipeptide…”. X-ray diffraction, 3 ligands (2OP, DVA, VAD), 19 pockets (best druggability 0.74). MolNFT v1 #147417 on GenesisL1: 3D…
- PDB
- 6ECF
- Type
- protein
- Length
- 1,546 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VLM2; Dodecadepsipeptide
- EC
- 3.1.2.-
- UniProt
- Q1PSF3
- Ligands
- 2OP, DVA, VAD
- Pockets
- 19 · best druggability 0.74
Structure
x-ray diffraction · 7 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VLM2 (EC 3.1.2.-) | protein | 251 | 47% helix, 16% strand | Q1PSF3 |
| B | VLM2 (EC 3.1.2.-) | protein | 252 | 46% helix, 15% strand | Q1PSF3 |
| C | VLM2 (EC 3.1.2.-) | protein | 252 | 45% helix, 16% strand | Q1PSF3 |
| D | VLM2 (EC 3.1.2.-) | protein | 265 | 43% helix, 14% strand | Q1PSF3 |
| E | VLM2 (EC 3.1.2.-) | protein | 262 | 46% helix, 13% strand | Q1PSF3 |
| F | VLM2 (EC 3.1.2.-) | protein | 258 | 45% helix, 14% strand | Q1PSF3 |
| G, I, H, K, J, L | Dodecadepsipeptide | protein | 1 | 0% helix, 0% strand | — |
Ligands and binding sites
- 2OP · (2S)-2-hydroxypropanoic acid · ligand · 6 copies · chains A, G, B, I, C, H, D, K, E, J, F, L
- DVA · D-valine · ligand · 2 copies · chains A, G, B, I
- VAD · Deaminohydroxyvaline · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 984 | 0.74 | 0.77 | 62 | 2OP |
| 2 | 1070 | 0.74 | 0.77 | 89 | empty |
| 3 | 611 | 0.69 | 0.77 | 34 | 2OP |
| 4 | 537 | 0.67 | 0.77 | 36 | VAD, DVA, 2OP |
| 5 | 594 | 0.66 | 0.76 | 42 | 2OP |
Interfaces
14 interfaces between chains.
- A–C · 799 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 774 Ų buried · 19 hydrogen bonds · protein-protein
- A–E · 769 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 759 Ų buried · 3 hydrogen bonds · protein-protein
- B–F · 696 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent, 6 modified (covalent ligand, nonstandard).
Compared structures
- 6ECF · Vlm2 thioesterase domain with genetically encoded 2,3-diaminopropionic acid bound with a… · 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 Q1PSF3
- Elsewhere: RCSB PDB 6ECF · PDBe 6ECF · UniProt Q1PSF3
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