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
- 3LJT
- Type
- protein
- Length
- 218 residues
- Chains
- 1
- 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
- LA3, CA, ZN
- Pockets
- 2 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 39% 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 | 218 | 39% helix, 16% strand | Q9UNA0 |
Ligands and binding sites
- LA3 · (2R)-2-[4-(1,3-benzodioxol-5-yl)benzyl]-N~4~-hydroxy-N~1~-[(1S,2R)-2-hydroxy-2,3-dihydro-1H-inden-1-yl]butanediamide · ligand · chains A
- CA · Calcium ion · metal · 3 copies · chains A
- ZN · Zinc ion · metal · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 230 | 0.53 | 0.77 | 29 | LA3 |
| 2 | 60 | 0.38 | 0.80 | 15 | empty |
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3LJT · 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 0.95
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 3LJT · PDBe 3LJT · UniProt Q9UNA0
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