MolNFT v1 · #161567 · protein
Metalloproteinase
6QIG · Antibody light chain: “Metalloproteinase”. X-ray diffraction, 7 ligands (NAG, BMA, MAN), 15 pockets (best druggability 0.71). MolNFT v1 #161567 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6QIG
- Type
- protein
- Length
- 1,021 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody light chain; Antibody heavy chain; A disintegrin and metalloproteinase with…
- EC
- 3.4.24.87
- UniProt
- Q76LX8
- Ligands
- NAG, BMA, MAN, FUC, CA, ZN, CL
- Pockets
- 15 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Antibody light chain | protein | 213 | 7% helix, 53% strand | — |
| H | Antibody heavy chain | protein | 227 | 7% helix, 47% strand | — |
| A | A disintegrin and metalloproteinase with thrombospondin motifs 13 (EC 3.4.24.87) | protein | 581 | 17% helix, 24% strand | Q76LX8 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains H, A
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains H
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains H
- FUC · alpha-L-fucopyranose · sugar · chains A
- CA · Calcium ion · metal · 3 copies · chains A
- ZN · Zinc ion · metal · chains A
- CL · Chloride ion · ion · 5 copies · chains L, H, A
- PEG · Di(hydroxyethyl)ether · additive · 8 copies · chains L, H, A
- GOL · Glycerol · additive · 2 copies · chains L, H, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 268 | 0.71 | 0.85 | 33 | CL |
| 2 | 286 | 0.70 | 0.84 | 60 | ZN |
| 3 | 596 | 0.64 | 0.75 | 56 | PEG |
| 4 | 353 | 0.63 | 0.79 | 55 | PEG |
| 5 | 270 | 0.59 | 0.78 | 36 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1975 Ų buried · 14 hydrogen bonds · protein-protein
- H–A · 944 Ų buried · 14 hydrogen bonds · protein-protein
- L–A · 75 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 19 disulfide, 7 glycan (disulfide, N-glycosylation, O-glycosylation).
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 Q76LX8
- Elsewhere: RCSB PDB 6QIG · PDBe 6QIG · UniProt Q76LX8
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