MolNFT v1 · #72630 · protein
Crystal structure of toxoplasma gondii profilin
3NEC · Inflammatory profilin: “Crystal structure of toxoplasma gondii profilin”. X-ray diffraction, 2 ligands (DTV, SO4), 7 pockets (best druggability 0.80). MolNFT v1 #72630 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3NEC
- Type
- protein
- Length
- 658 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inflammatory profilin
- UniProt
- Q58NA1
- Ligands
- DTV, SO4
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inflammatory profilin | protein | 162 | 28% helix, 41% strand | Q58NA1 |
| B | Inflammatory profilin | protein | 164 | 27% helix, 41% strand | Q58NA1 |
| C, D | Inflammatory profilin | protein | 166 | 27% helix, 40% strand | Q58NA1 |
Ligands and binding sites
- DTV · (2S,3S)-1,4-dimercaptobutane-2,3-diol · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1037 | 0.80 | 0.82 | 123 | empty |
| 2 | 198 | 0.58 | 0.81 | 38 | empty |
| 3 | 85 | 0.46 | 0.81 | 25 | empty |
| 4 | 68 | 0.41 | 0.80 | 20 | empty |
| 5 | 57 | 0.33 | 0.77 | 15 | empty |
Interfaces
5 interfaces between chains.
- C–D · 616 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 400 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 397 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 391 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 47 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 modified (engineered).
Compared structures
- 3NEC · Crystal Structure of Toxoplasma gondii Profilin · 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 Q58NA1
- Elsewhere: RCSB PDB 3NEC · PDBe 3NEC · UniProt Q58NA1
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