MolNFT v1 · #50489 · protein

Crystal structure of ADAMTS5 with inhibitor bound

2RJQ · Adamts-5: “Crystal structure of ADAMTS5 with inhibitor bound”. X-ray diffraction, 5 ligands (BAT, NAG, ZN), 3 pockets (best druggability 0.64). MolNFT v1 #50489 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2RJQ
Type: protein
Length: 292 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Adamts-5
EC: 3.4.24.-
UniProt: Q9UNA0
Ligands: BAT, NAG, ZN, CA, CL
Pockets: 3 · best druggability 0.64

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Adamts-5 (EC 3.4.24.-)	protein	292	30% helix, 19% strand	Q9UNA0

Ligands and binding sites

BAT · 4-(N-hydroxyamino)-2R-isobutyl-2S-(2-thienylthiomethyl)succinyl-L-phenylalanine-N-methylamide · ligand · chains A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
ZN · Zinc ion · metal · 2 copies · chains A
CA · Calcium ion · metal · 2 copies · chains A
CL · Chloride ion · ion · 2 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	250	0.64	0.82	32	empty
2	126	0.46	0.78	17	BAT
3	53	0.36	0.80	15	empty

Modifications

Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

2RJQ · Crystal structure of ADAMTS5 with inhibitor bound · 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 0.99

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 2RJQ · PDBe 2RJQ · UniProt Q9UNA0

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