MolNFT v1 · #47352 · protein
Mmp-9 active site mutant with phosphinate inhibitor
2OVZ · Matrix metalloproteinase-9 (ec 3.4.24.35) (mmp-9) (92 kda…: “Mmp-9 active site mutant with phosphinate inhibitor”. X-ray diffraction, 4 ligands (5MR, CA, ZN), 5 pockets (best druggability 0.58). MolNFT v1 #47352 on GenesisL1: 3D…
- PDB
- 2OVZ
- Type
- protein
- Length
- 314 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Matrix metalloproteinase-9 (ec 3.4.24.35) (mmp-9) (92 kda type IV collagenase) (92 kda…
- EC
- 3.4.24.35
- UniProt
- P14780
- Ligands
- 5MR, CA, ZN, CL
- Pockets
- 5 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Matrix metalloproteinase-9 (ec 3.4.24.35) (mmp-9) (92 kda type IV collagenase) (92 kda gelatinase) (gelatinase B) (gelb) (EC 3.4.24.35) | protein | 159 | 24% helix, 17% strand | P14780 |
| B | Matrix metalloproteinase-9 (ec 3.4.24.35) (mmp-9) (92 kda type IV collagenase) (92 kda gelatinase) (gelatinase B) (gelb) (EC 3.4.24.35) | protein | 155 | 25% helix, 17% strand | P14780 |
Ligands and binding sites
- 5MR · Nalpha-{(2S)-3-[(S)-hydroxy(phenyl)phosphoryl]-2-[(3-phenylisoxazol-5-yl)methyl]propanoyl}-L-tryptophanamide · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 10 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 189 | 0.58 | 0.81 | 33 | ZN, 5MR |
| 2 | 120 | 0.57 | 0.84 | 24 | 5MR |
| 3 | 230 | 0.54 | 0.77 | 37 | CL |
| 4 | 60 | 0.51 | 0.86 | 20 | empty |
| 5 | 90 | 0.42 | 0.79 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 528 Ų buried · 7 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 2OVZ · PDBe 2OVZ · UniProt P14780
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