Research workbench
Adam-8 metalloproteinase domain with bound batimastat
Analyse Adam-8 metalloproteinase domain with bound batimastat in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DD8
- Type
- protein
- Length
- 815 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Disintegrin and metalloproteinase domain-containing protein 8
- EC
- 3.4.24.-
- UniProt
- P78325
- Ligands
- BAT, NA, CA, ZN, K, CL
- Pockets
- 6 · best druggability 0.63
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Disintegrin and metalloproteinase domain-containing protein 8 (EC 3.4.24.-) | protein | 201 | 38% helix, 16% strand | P78325 |
| B | Disintegrin and metalloproteinase domain-containing protein 8 (EC 3.4.24.-) | protein | 205 | 38% helix, 16% strand | P78325 |
| C | Disintegrin and metalloproteinase domain-containing protein 8 (EC 3.4.24.-) | protein | 201 | 37% helix, 16% strand | P78325 |
| D | Disintegrin and metalloproteinase domain-containing protein 8 (EC 3.4.24.-) | protein | 208 | 37% helix, 16% strand | P78325 |
Ligands and binding sites
- BAT · 4-(N-hydroxyamino)-2R-isobutyl-2S-(2-thienylthiomethyl)succinyl-L-phenylalanine-N-methylamide · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 8 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- K · Potassium ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 474 | 0.63 | 0.77 | 52 | BAT, ZN, CL |
| 2 | 402 | 0.61 | 0.77 | 55 | BAT, ZN, NA, CL |
| 3 | 273 | 0.56 | 0.77 | 33 | empty |
| 4 | 98 | 0.44 | 0.79 | 23 | BAT, ZN, NA, CL |
| 5 | 65 | 0.43 | 0.82 | 22 | BAT, ZN, NA |
Interfaces
4 interfaces between chains.
- A–B · 377 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 299 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 132 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 36 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 4DD8 · ADAM-8 metalloproteinase domain with bound batimastat · the same entry in another collection · chain D against D, TM-score 1.00
- P78325 · AlphaFold monomer V2.0 prediction for disintegrin and metalloproteinase domain-containing… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P78325
- Elsewhere: RCSB PDB 4DD8 · PDBe 4DD8 · UniProt P78325
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.