Research workbench
Crystal structure of human matrix metalloproteinase MMP9 (gelatinase B).
Analyse Crystal structure of human matrix metalloproteinase MMP9 (gelatinase B). in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1L6J
- Type
- protein
- Length
- 405 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Matrix metalloproteinase-9
- EC
- 3.4.24.35
- UniProt
- P14780
- Ligands
- CA, ZN
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 20% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Matrix metalloproteinase-9 (EC 3.4.24.35) | protein | 405 | 20% helix, 19% strand | P14780 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 97 | 0.63 | 0.89 | 20 | empty |
| 2 | 438 | 0.59 | 0.75 | 51 | CA |
| 3 | 145 | 0.46 | 0.77 | 17 | empty |
| 4 | 75 | 0.45 | 0.81 | 16 | empty |
| 5 | 73 | 0.33 | 0.75 | 21 | empty |
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1L6J · Crystal structure of human matrix metalloproteinase MMP9 (gelatinase B). · 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 A against A, TM-score 0.87
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 1L6J · PDBe 1L6J · UniProt P14780
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