Research workbench
Complex of 3-mercapto-2-benzylpropanoyl-ala-gly-NH2 with the catalytic domain of matrix metallo proteinase-8 (MET80 form)
Analyse Complex of 3-mercapto-2-benzylpropanoyl-ala-gly-NH2 with the catalytic domain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JAO
- Type
- protein
- Length
- 158 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Matrix metallo proteinase-8 (MET80 form)
- EC
- 3.4.24.34
- UniProt
- P22894
- Ligands
- 0D3, CA, ZN
- Pockets
- 2 · best druggability 0.54
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Matrix metallo proteinase-8 (MET80 form) (EC 3.4.24.34) | protein | 158 | 24% helix, 16% strand | P22894 |
Ligands and binding sites
- 0D3 · N-[(2S)-2-benzyl-3-sulfanylpropanoyl]-L-alanylglycinamide · ligand · chains A
- CA · Calcium ion · metal · 2 copies · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 94 | 0.54 | 0.84 | 21 | 0D3, ZN |
| 2 | 52 | 0.28 | 0.75 | 15 | empty |
Compared structures
- 1JAO · Complex of 3-mercapto-2-benzylpropanoyl-ala-gly-NH2 with the catalytic domain of matrix… · the same entry in another collection · chain A against A, TM-score 1.00
- P22894 · AlphaFold monomer V2.0 prediction for neutrophil collagenase (P22894) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P22894
- Elsewhere: RCSB PDB 1JAO · PDBe 1JAO · UniProt P22894
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