MolNFT v1 · #69786 · protein
Crystal structure of catalytic domain of tace with the first hydantoin inhibitor occupying the S1' pocket
3L0V · Disintegrin and metalloproteinase domain-containing protein…: “Crystal structure of catalytic domain of tace with the first hydantoin inhibitor occupying the S1' pocket”. X-ray diffraction, 2 ligands (724, ZN), 4 pockets (best…
- PDB
- 3L0V
- Type
- protein
- Length
- 507 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Disintegrin and metalloproteinase domain-containing protein 17
- EC
- 3.4.24.86
- UniProt
- P78536
- Ligands
- 724, ZN
- Pockets
- 4 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Disintegrin and metalloproteinase domain-containing protein 17 (EC 3.4.24.86) | protein | 255 | 34% helix, 17% strand | P78536 |
| B | Disintegrin and metalloproteinase domain-containing protein 17 (EC 3.4.24.86) | protein | 252 | 32% helix, 19% strand | P78536 |
Ligands and binding sites
- 724 · (5R)-5-[(5-methoxy-3-oxo-1,3-dihydro-2H-indazol-2-yl)methyl]-5-methylimidazolidine-2,4-dione · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 248 | 0.51 | 0.75 | 33 | empty |
| 2 | 152 | 0.49 | 0.78 | 30 | 724 |
| 3 | 115 | 0.47 | 0.79 | 19 | 724 |
| 4 | 72 | 0.30 | 0.73 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 201 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3L0V · Crystal structure of catalytic domain of TACE with the first hydantoin inhibitor… · the same entry in another collection · chain A against A, TM-score 1.00
- P78536 · AlphaFold monomer V2.0 prediction for disintegrin and metalloproteinase domain-containing… · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P78536
- Elsewhere: RCSB PDB 3L0V · PDBe 3L0V · UniProt P78536
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