MolNFT v1 · #143931 · protein
ADAM10 extracellular domain
6BE6 · Disintegrin and metalloproteinase domain-containing protein…: “ADAM10 extracellular domain”. X-ray diffraction, 5 ligands (MAN, NAG, ZN), 20 pockets (best druggability 0.82). MolNFT v1 #143931 on GenesisL1: 3D structure, binding…
- PDB
- 6BE6
- Type
- protein
- Length
- 1,728 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Disintegrin and metalloproteinase domain-containing protein 10
- EC
- 3.4.24.81
- UniProt
- O14672
- Ligands
- MAN, NAG, ZN, CA, SO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 23% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Disintegrin and metalloproteinase domain-containing protein 10 (EC 3.4.24.81) | protein | 431 | 23% helix, 21% strand | O14672 |
| C | Disintegrin and metalloproteinase domain-containing protein 10 (EC 3.4.24.81) | protein | 433 | 22% helix, 19% strand | O14672 |
| D | Disintegrin and metalloproteinase domain-containing protein 10 (EC 3.4.24.81) | protein | 433 | 24% helix, 18% strand | O14672 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 17 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 784 | 0.82 | 0.85 | 93 | empty |
| 2 | 762 | 0.81 | 0.85 | 102 | empty |
| 3 | 1082 | 0.78 | 0.80 | 116 | empty |
| 4 | 704 | 0.77 | 0.82 | 75 | empty |
| 5 | 187 | 0.69 | 0.87 | 40 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1386 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1375 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 980 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 879 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 68 disulfide, 4 glycan (disulfide, N-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 O14672
- Elsewhere: RCSB PDB 6BE6 · PDBe 6BE6 · UniProt O14672
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