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Crystal structure of the catalytic domain of human MMP12 in complex with a selective carboxylate based inhibitor.
Analyse Crystal structure of the catalytic domain of human MMP12 in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4H84
- Type
- protein
- Length
- 318 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Macrophage metalloelastase
- EC
- 3.4.24.65
- UniProt
- P39900
- Ligands
- Y38, CA, ZN
- Pockets
- 2 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Macrophage metalloelastase (EC 3.4.24.65) | protein | 159 | 26% helix, 17% strand | P39900 |
Ligands and binding sites
- Y38 · N-[2-(benzoylamino)ethyl]-N-(biphenyl-4-ylsulfonyl)-D-valine · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 6 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- PGO · S-1,2-propanediol · additive · 7 copies · chains A, B
- GOL · Glycerol · additive · 7 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
- PGR · R-1,2-propanediol · additive · 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 | 1152 | 0.82 | 0.83 | 91 | Y38, PGO, PEG, GOL |
| 2 | 66 | 0.31 | 0.74 | 19 | PGO |
Interfaces
1 interface between chains.
- A–B · 511 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4H84 · Crystal structure of the catalytic domain of Human MMP12 in complex with a selective… · the same entry in another collection · chain A against A, TM-score 1.00
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 P39900
- Elsewhere: RCSB PDB 4H84 · PDBe 4H84 · UniProt P39900
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