Research workbench
Complex of pro-leu-gly-hydroxylamine with the catalytic domain of matrix metallo proteinase-8 (MET80 form)
Analyse Complex of pro-leu-gly-hydroxylamine with the catalytic domain of matrix… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JAP
- Type
- protein
- Length
- 160 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Matrix metallo proteinase-8 (MET80 form); Pro-leu-gly-hydroxylamine
- EC
- 3.4.24.34
- UniProt
- P22894
- Ligands
- HOA, CA, ZN
- Pockets
- 2 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 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 | 157 | 24% helix, 16% strand | P22894 |
| I | Pro-leu-gly-hydroxylamine | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- HOA · Hydroxyamine · ligand · chains A, I
- CA · Calcium ion · metal · 2 copies · chains A
- ZN · Zinc ion · metal · 2 copies · chains A, I
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 | 76 | 0.53 | 0.86 | 19 | empty |
| 2 | 50 | 0.28 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–I · 265 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 1JAP · Complex of pro-leu-gly-hydroxylamine with the catalytic domain of matrix metallo… · the same entry in another collection · chain I against I, 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 1JAP · PDBe 1JAP · UniProt P22894
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