MolNFT v1 · #7891 · protein
MMP9-inhibitor complex
1GKC · 92 kda type IV collagenase: “MMP9-inhibitor complex”. X-ray diffraction, 3 ligands (NFH, CA, ZN), 3 pockets (best druggability 0.70). MolNFT v1 #7891 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1GKC
- Type
- protein
- Length
- 315 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 92 kda type IV collagenase
- EC
- 3.4.24.35
- UniProt
- P14780
- Ligands
- NFH, CA, ZN
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 92 kda type IV collagenase (EC 3.4.24.35) | protein | 159 | 24% helix, 17% strand | P14780 |
| B | 92 kda type IV collagenase (EC 3.4.24.35) | protein | 156 | 24% helix, 17% strand | P14780 |
Ligands and binding sites
- NFH · N~2~-[(2R)-2-{[formyl(hydroxy)amino]methyl}-4-methylpentanoyl]-N,3-dimethyl-L-valinamide · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 10 copies · chains A, B
- ZN · Zinc ion · metal · 4 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 73 | 0.70 | 0.95 | 23 | empty |
| 2 | 138 | 0.58 | 0.83 | 25 | NFH, ZN |
| 3 | 145 | 0.55 | 0.81 | 24 | NFH |
Interfaces
1 interface between chains.
- A–B · 706 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
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 P14780
- Elsewhere: RCSB PDB 1GKC · PDBe 1GKC · UniProt P14780
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