Research workbench
Crystal structure of the catalytic domain of adamts-5 in complex with an amino-2-indanol compound
Analyse Crystal structure of the catalytic domain of adamts-5 in complex with an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HYG
- Type
- protein
- Length
- 434 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
- 099, CA, ZN
- Pockets
- 3 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | A disintegrin and metalloproteinase with thrombospondin motifs 5 (EC 3.4.24.-) | protein | 217 | 37% helix, 16% strand | Q9UNA0 |
Ligands and binding sites
- 099 · (2R)-N~4~-hydroxy-2-(3-hydroxybenzyl)-N~1~-[(1S,2R)-2-hydroxy-2,3-dihydro-1H-inden-1-yl]butanediamide · 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 | 202 | 0.59 | 0.81 | 25 | ZN, 099 |
| 2 | 228 | 0.57 | 0.79 | 25 | ZN, 099 |
| 3 | 206 | 0.42 | 0.72 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 113 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3HYG · Crystal Structure of the Catalytic Domain of ADAMTS-5 in Complex with an Amino-2-indanol… · 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 3HYG · PDBe 3HYG · UniProt Q9UNA0
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