Research workbench
Crystal structure of the catalytic domain of mmp-13 complexed with a potent pyrimidinetrione inhibitor
Analyse Crystal structure of the catalytic domain of mmp-13 complexed with a potent… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YOU
- Type
- protein
- Length
- 333 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Collagenase 3
- EC
- 3.4.24.-
- UniProt
- P45452
- Ligands
- PFD, ZN, CA, SO4
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Collagenase 3 (EC 3.4.24.-) | protein | 168 | 25% helix, 18% strand | P45452 |
| B | Collagenase 3 (EC 3.4.24.-) | protein | 165 | 25% helix, 18% strand | P45452 |
Ligands and binding sites
- PFD · 5-(2-ethoxyethyl)-5-[4-(4-fluorophenoxy)phenoxy]pyrimidine-2,4,6(1H,3H,5H)-trione · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 923 | 0.73 | 0.77 | 71 | ZN, PFD |
| 2 | 162 | 0.55 | 0.80 | 24 | PFD |
| 3 | 54 | 0.34 | 0.78 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1148 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 1YOU · Crystal structure of the catalytic domain of MMP-13 complexed with a potent… · the same entry in another collection · chain A against A, TM-score 1.00
- P45452 · AlphaFold monomer V2.0 prediction for collagenase 3 (P45452) · 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 P45452
- Elsewhere: RCSB PDB 1YOU · PDBe 1YOU · UniProt P45452
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