MolNFT v1 · #81579 · protein
MMP12 in a complex with the dimeric adduct: 5-(5-phenylhydantoin)-5- phenylhydantoin
3UVC · Macrophage metalloelastase: “MMP12 in a complex with the dimeric adduct: 5-(5-phenylhydantoin)-5- phenylhydantoin”. X-ray diffraction, 4 ligands (0D2, CA, ZN), 3 pockets (best druggability 0.78). MolNFT v1 #81579 on GenesisL1: 3D…
- PDB
- 3UVC
- Type
- protein
- Length
- 316 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
- 0D2, CA, ZN, CL
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Macrophage metalloelastase (EC 3.4.24.65) | protein | 158 | 27% helix, 17% strand | P39900 |
Ligands and binding sites
- 0D2 · (4R,4'S)-4,4'-diphenyl-4,4'-biimidazolidine-2,2',5,5'-tetrone · ligand · chains A, B
- CA · Calcium ion · metal · 7 copies · chains A, B
- ZN · Zinc ion · metal · 6 copies · chains A, B
- CL · Chloride ion · ion · 6 copies · chains A, B
- IMD · Imidazole · additive · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 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 | 860 | 0.78 | 0.81 | 78 | ZN, IMD, 0D2, EDO, CL |
| 2 | 228 | 0.52 | 0.76 | 31 | IMD |
| 3 | 71 | 0.34 | 0.75 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 368 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3UVC · MMP12 in a complex with the dimeric adduct: 5-(5-phenylhydantoin)-5-phenylhydantoin · 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 3UVC · PDBe 3UVC · UniProt P39900
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