MolNFT v1 · #137413 · protein
M.TB antigen 85C acyl-enzyme intermediate with tetrahydrolipstatin
5VNS · Diacylglycerol ACYLTRANSFERASE/MYCOLYLTRANSFERASE AG85C: “M.TB antigen 85C acyl-enzyme intermediate with tetrahydrolipstatin”. X-ray diffraction, 1 ligand (DH9), 2 pockets (best druggability 0.55). MolNFT v1 #137413 on GenesisL1: 3D…
- PDB
- 5VNS
- Type
- protein
- Length
- 276 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Diacylglycerol ACYLTRANSFERASE/MYCOLYLTRANSFERASE AG85C
- EC
- 2.3.1.122, 2.3.1.20
- UniProt
- P9WQN8
- Ligands
- DH9
- Pockets
- 2 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Diacylglycerol ACYLTRANSFERASE/MYCOLYLTRANSFERASE AG85C (EC 2.3.1.122, 2.3.1.20) | protein | 276 | 39% helix, 17% strand | P9WQN8 |
Ligands and binding sites
- DH9 · (2S,3S,5S)-5-[(N-formyl-L-leucyl)oxy]-2-hexyl-3-hydroxyhexadecanoic acid · ligand · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A
- GOL · Glycerol · additive · 2 copies · chains A
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 | 238 | 0.55 | 0.77 | 29 | DH9, GOL |
| 2 | 51 | 0.31 | 0.77 | 15 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5VNS · M.tb Antigen 85C Acyl-Enzyme Intermediate with Tetrahydrolipstatin · the same entry in another collection · chain A against A, TM-score 1.00
- P9WQN8 · AlphaFold monomer V2.0 prediction for diacylglycerol ACYLTRANSFERASE/MYCOLYLTRANSFERASE… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P9WQN8
- Elsewhere: RCSB PDB 5VNS · PDBe 5VNS · UniProt P9WQN8
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