MolNFT v1 · #11326 · protein
Crystal structure of MMP8-barbiturate complex reveals mechanism for collagen substrate recognition
1JJ9 · Matrix metalloproteinase 8: “Crystal structure of MMP8-barbiturate complex reveals mechanism for collagen substrate recognition”. X-ray diffraction, 3 ligands (BBT, CA, ZN), 1 pocket (best druggability 0.49). MolNFT v1 #11326 on…
- PDB
- 1JJ9
- Type
- protein
- Length
- 158 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Matrix metalloproteinase 8
- EC
- 3.4.24.34
- UniProt
- P22894
- Ligands
- BBT, CA, ZN
- Pockets
- 1 · best druggability 0.49
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Matrix metalloproteinase 8 (EC 3.4.24.34) | protein | 158 | 25% helix, 16% strand | P22894 |
Ligands and binding sites
- BBT · 2-hydroxy-5-[4-(2-hydroxy-ethyl)-piperidin-1-yl]-5-phenyl-1H-pyrimidine-4,6-dione · 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
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 95 | 0.49 | 0.82 | 20 | BBT |
Compared structures
- 1JJ9 · Crystal Structure of MMP8-Barbiturate Complex Reveals Mechanism for Collagen Substrate… · 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 1JJ9 · PDBe 1JJ9 · UniProt P22894
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