MolNFT v1 · #125159 · protein
Crystal structure of the complex between ADAM10 D+C domain and a conformation specific mab 8C7.
5L0Q · Disintegrin and metalloproteinase domain-containing protein…: “Crystal structure of the complex between ADAM10 D+C domain and a conformation specific mab 8C7.”. X-ray diffraction, 3 ligands (NAG, MG, SO4), 11 pockets (best…
- PDB
- 5L0Q
- Type
- protein
- Length
- 1,249 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Disintegrin and metalloproteinase domain-containing protein 10; Mab 8C7 light chain; Mab…
- EC
- 3.4.24.81
- UniProt
- Q10741
- Ligands
- NAG, MG, SO4
- Pockets
- 11 · best druggability 0.64
Structure
x-ray diffraction · 5 distinct chains · 6% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Disintegrin and metalloproteinase domain-containing protein 10 (EC 3.4.24.81) | protein | 203 | 7% helix, 18% strand | Q10741 |
| B, E | Mab 8C7 light chain | protein | 212 | 7% helix, 50% strand | — |
| C | Mab 8C7 heavy chain | protein | 213 | 6% helix, 54% strand | — |
| D | Disintegrin and metalloproteinase domain-containing protein 10 (EC 3.4.24.81) | protein | 195 | 8% helix, 19% strand | Q10741 |
| F | Mab 8C7 heavy chain | protein | 214 | 4% helix, 55% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, C, D, F
- MG · Magnesium ion · metal · 2 copies · chains A, D
- SO4 · Sulfate ion · ion · 13 copies · chains A, C, B, D, F, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 631 | 0.64 | 0.75 | 70 | empty |
| 2 | 625 | 0.64 | 0.75 | 62 | empty |
| 3 | 55 | 0.41 | 0.82 | 21 | empty |
| 4 | 128 | 0.39 | 0.74 | 27 | SO4 |
| 5 | 98 | 0.36 | 0.74 | 15 | SO4 |
Interfaces
7 interfaces between chains.
- E–F · 1946 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 1938 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 581 Ų buried · 10 hydrogen bonds · protein-protein
- D–F · 510 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 346 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 36 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5L0Q · Crystal structure of the complex between ADAM10 D+C domain and a conformation specific… · the same entry in another collection · chain F against F, TM-score 1.00
- Q10741 · AlphaFold monomer V2.0 prediction for disintegrin and metalloproteinase domain-containing… · a predicted model of the same protein · chain D against A, TM-score 0.90
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 Q10741
- Elsewhere: RCSB PDB 5L0Q · PDBe 5L0Q · UniProt Q10741
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