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Crystal structure of catalytic domain of tace with phenyl- pyrrolidinyl-tartrate inhibitor
Analyse Crystal structure of catalytic domain of tace with phenyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KME
- Type
- protein
- Length
- 507 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, Z59, ZN
- Pockets
- 5 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | TNF-alpha-converting enzyme (EC 3.4.24.86) | protein | 253 | 34% 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
- Z59 · (2R,3R)-2,3-dihydroxy-4-oxo-4-[(2R)-2-phenylpyrrolidin-1-yl]-N-(thiophen-2-ylmethyl)butanamide · ligand · chains B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- IPA · Isopropyl alcohol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 158 | 0.55 | 0.81 | 27 | Z59 |
| 2 | 168 | 0.53 | 0.79 | 28 | ZN, INN |
| 3 | 295 | 0.53 | 0.75 | 27 | empty |
| 4 | 64 | 0.30 | 0.74 | 11 | empty |
| 5 | 64 | 0.29 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 56 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3KME · Crystal structure of catalytic domain of TACE with phenyl-pyrrolidinyl-tartrate 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 0.97
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 3KME · PDBe 3KME · UniProt P78536
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