Research workbench
Crystal structure of catalytic domain of tace with the first hydantoin inhibitor occupying the S1' pocket
Analyse Crystal structure of catalytic domain of tace with the first hydantoin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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