Research workbench
Endogenous-like inhibitory antibodies targeting activated metalloproteinase motifs show therapeutic potential
Analyse Endogenous-like inhibitory antibodies targeting activated metalloproteinase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UTZ
- Type
- protein
- Length
- 1,283 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metalloproteinase, light chain; Metalloproteinase, heavy chain
- Ligands
- SO4
- Pockets
- 13 · best druggability 0.62
Structure
x-ray diffraction · 6 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metalloproteinase, light chain | protein | 215 | 7% helix, 52% strand | — |
| B | Metalloproteinase, heavy chain | protein | 217 | 8% helix, 52% strand | — |
| D | Metalloproteinase, light chain | protein | 212 | 6% helix, 52% strand | — |
| C | Metalloproteinase, heavy chain | protein | 214 | 8% helix, 53% strand | — |
| E | Metalloproteinase, light chain | protein | 212 | 7% helix, 51% strand | — |
| F | Metalloproteinase, heavy chain | protein | 213 | 7% helix, 53% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 10 copies · chains B, F, A, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 581 | 0.62 | 0.74 | 54 | empty |
| 2 | 466 | 0.58 | 0.74 | 49 | empty |
| 3 | 370 | 0.58 | 0.75 | 35 | SO4 |
| 4 | 243 | 0.57 | 0.78 | 42 | empty |
| 5 | 105 | 0.56 | 0.84 | 15 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1775 Ų buried · 16 hydrogen bonds · protein-protein
- D–C · 1677 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 1659 Ų buried · 15 hydrogen bonds · protein-protein
- B–F · 577 Ų buried · 4 hydrogen bonds · protein-protein
- C–F · 437 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 3UTZ · Endogenous-like inhibitory antibodies targeting activated metalloproteinase motifs show… · 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
- Elsewhere: RCSB PDB 3UTZ · PDBe 3UTZ
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