MolNFT v1 · #72571 · protein
Crystal structure of mt-SP1 bound to benzamidine phosphonate inhibitor
3NCL · Suppressor of tumorigenicity 14 protein: “Crystal structure of mt-SP1 bound to benzamidine phosphonate inhibitor”. X-ray diffraction, 1 ligand (CCZ), 1 pocket (best druggability 0.46). MolNFT v1 #72571 on GenesisL1: 3D structure…
- PDB
- 3NCL
- Type
- protein
- Length
- 241 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Suppressor of tumorigenicity 14 protein
- EC
- 3.4.21.109
- UniProt
- Q9Y5Y6
- Ligands
- CCZ
- Pockets
- 1 · best druggability 0.46
Structure
x-ray diffraction · 1 distinct chain · 10% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Suppressor of tumorigenicity 14 protein (EC 3.4.21.109) | protein | 241 | 10% helix, 36% strand | Q9Y5Y6 |
Ligands and binding sites
- CCZ · phenyl (4-carbamimidoylbenzyl)phosphonate · ligand · chains A
- FMT · Formic acid · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 185 | 0.46 | 0.75 | 37 | CCZ |
Modifications
Observed in the structure: 3 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 3NCL · Crystal Structure of MT-SP1 bound to Benzamidine Phosphonate Inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y5Y6 · AlphaFold monomer V2.0 prediction for suppressor of tumorigenicity 14 protein (Q9Y5Y6) · 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 Q9Y5Y6
- Elsewhere: RCSB PDB 3NCL · PDBe 3NCL · UniProt Q9Y5Y6
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