MolNFT v1 · #47353 · protein
Mmp-9 active site mutant with iodine-labeled carboxylate inhibitor
2OW0 · Matrix metalloproteinase-9 (mmp-9) (92 kda type IV…: “Mmp-9 active site mutant with iodine-labeled carboxylate inhibitor”. X-ray diffraction, 4 ligands (6MR, CA, ZN), 4 pockets (best druggability 0.61). MolNFT v1 #47353 on…
- PDB
- 2OW0
- Type
- protein
- Length
- 314 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Matrix metalloproteinase-9 (mmp-9) (92 kda type IV collagenase) (92 kda gelatinase)…
- EC
- 3.4.24.35
- UniProt
- P14780
- Ligands
- 6MR, CA, ZN, CL
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Matrix metalloproteinase-9 (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 (mmp-9) (92 kda type IV collagenase) (92 kda gelatinase) (gelatinase B) (gelb) (EC 3.4.24.35) | protein | 155 | 25% helix, 18% strand | P14780 |
Ligands and binding sites
- 6MR · N-[(4'-iodobiphenyl-4-yl)sulfonyl]-D-tryptophan · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 8 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 174 | 0.61 | 0.83 | 24 | 6MR |
| 2 | 212 | 0.60 | 0.81 | 31 | 6MR |
| 3 | 227 | 0.57 | 0.79 | 29 | CL |
| 4 | 58 | 0.35 | 0.78 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 541 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 2OW0 · MMP-9 active site mutant with iodine-labeled carboxylate inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- P14780 · AlphaFold monomer V2.0 prediction for matrix metalloproteinase-9 (P14780) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 2OW0 · PDBe 2OW0 · UniProt P14780
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