Research workbench
Crystal structure of catalytic domain of tace with hydantoin inhibitor
Analyse Crystal structure of catalytic domain of tace with hydantoin inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3L0T
- Type
- protein
- Length
- 508 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
- INN, Z94, ZN
- Pockets
- 6 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 32% 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 | 254 | 31% helix, 17% strand | P78536 |
| B | Disintegrin and metalloproteinase domain-containing protein 17 (EC 3.4.24.86) | protein | 254 | 33% helix, 18% strand | P78536 |
Ligands and binding sites
- INN · N-{(2R)-2-[2-(hydroxyamino)-2-oxoethyl]-4-methylpentanoyl}-3-methyl-L-valyl-N-(2-aminoethyl)-L-alaninamide · ligand · chains A
- Z94 · N-{4-[(4S)-2,5-dioxoimidazolidin-4-yl]phenyl}acetamide · ligand · chains B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- IPA · Isopropyl alcohol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 213 | 0.57 | 0.79 | 38 | ZN, INN |
| 2 | 126 | 0.46 | 0.78 | 24 | Z94 |
| 3 | 68 | 0.34 | 0.76 | 23 | empty |
| 4 | 97 | 0.33 | 0.73 | 19 | empty |
| 5 | 70 | 0.31 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 18 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3L0T · Crystal structure of catalytic domain of TACE with 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 A against A, TM-score 0.96
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 3L0T · PDBe 3L0T · UniProt P78536
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.