Research workbench
High resolution crystal structure of the catalytic domain of adamts-5 (aggrecanase-2)
Analyse High resolution crystal structure of the catalytic domain of adamts-5… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3B8Z
- Type
- protein
- Length
- 434 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein adamts-5
- EC
- 3.4.24.-
- UniProt
- Q9UNA0
- Ligands
- 294, CA, ZN
- Pockets
- 2 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein adamts-5 (EC 3.4.24.-) | protein | 217 | 37% helix, 16% strand | Q9UNA0 |
Ligands and binding sites
- 294 · N-hydroxy-4-({4-[4-(trifluoromethyl)phenoxy]phenyl}sulfonyl)tetrahydro-2H-pyran-4-carboxamide · 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
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 555 | 0.64 | 0.76 | 52 | ZN, 294 |
| 2 | 200 | 0.59 | 0.81 | 27 | 294 |
Interfaces
1 interface between chains.
- A–B · 131 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3B8Z · High Resolution Crystal Structure of the Catalytic Domain of ADAMTS-5 (Aggrecanase-2) · 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 A 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 3B8Z · PDBe 3B8Z · UniProt Q9UNA0
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