Research workbench
Crystal structure of the catalytic domain of adamts-5 in complex with the inhibitor GLPG1972
Analyse Crystal structure of the catalytic domain of adamts-5 in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YJM
- Type
- protein
- Length
- 429 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- A disintegrin and metalloproteinase with thrombospondin motifs 5
- EC
- 3.4.24.-
- UniProt
- Q9UNA0
- Ligands
- OU5, CA, ZN
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | A disintegrin and metalloproteinase with thrombospondin motifs 5 (EC 3.4.24.-) | protein | 217 | 36% helix, 16% strand | Q9UNA0 |
| B | A disintegrin and metalloproteinase with thrombospondin motifs 5 (EC 3.4.24.-) | protein | 212 | 38% helix, 17% strand | Q9UNA0 |
Ligands and binding sites
- OU5 · (5~{S})-5-[3-[(3~{S})-4-[3,5-bis(fluoranyl)phenyl]-3-methyl-piperazin-1-yl]-3-oxidanylidene-propyl]-5-cyclopropyl-imidazolidine-2,4-dione · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 6 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 627 | 0.69 | 0.77 | 70 | OU5 |
| 2 | 165 | 0.54 | 0.80 | 21 | ZN, OU5 |
| 3 | 55 | 0.36 | 0.79 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 656 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6YJM · Crystal Structure of the Catalytic Domain of ADAMTS-5 in Complex with the Inhibitor… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UNA0 · AlphaFold monomer V2.0 prediction for a disintegrin and metalloproteinase with… · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q9UNA0
- Elsewhere: RCSB PDB 6YJM · PDBe 6YJM · UniProt Q9UNA0
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