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Crystal structure of catalytic domain of tace with tartrate-based inhibitor
Analyse Crystal structure of catalytic domain of tace with tartrate-based inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KMC
- Type
- protein
- Length
- 509 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TNF-alpha-converting enzyme
- EC
- 3.4.24.86
- UniProt
- P78536
- Ligands
- INN, 403, ZN
- Pockets
- 6 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TNF-alpha-converting enzyme (EC 3.4.24.86) | protein | 255 | 33% helix, 17% strand | P78536 |
| B | TNF-alpha-converting enzyme (EC 3.4.24.86) | protein | 254 | 33% helix, 19% 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
- 403 · (2R,3R)-4-[4-(2-chlorophenyl)piperazin-1-yl]-2,3-dihydroxy-4-oxo-N-(2-thiophen-2-ylethyl)butanamide · ligand · chains 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
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 179 | 0.54 | 0.79 | 30 | 403 |
| 2 | 182 | 0.53 | 0.78 | 36 | ZN, INN |
| 3 | 73 | 0.32 | 0.74 | 14 | empty |
| 4 | 71 | 0.32 | 0.74 | 13 | empty |
| 5 | 72 | 0.31 | 0.75 | 18 | empty |
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3KMC · Crystal structure of catalytic domain of TACE with tartrate-based 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 3KMC · PDBe 3KMC · UniProt P78536
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