MolNFT v1 · #136406 · protein

Crystal structure of frizzled 5 crd in complex with pam

5URY · Frizzled-5: “Crystal structure of frizzled 5 crd in complex with pam”. X-ray diffraction, 3 ligands (PAM, FUC, NAG), 5 pockets (best druggability 0.41). MolNFT v1 #136406 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5URY
Type: protein
Length: 240 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Frizzled-5
UniProt: Q13467
Ligands: PAM, FUC, NAG
Pockets: 5 · best druggability 0.41

Structure

x-ray diffraction · 2 distinct chains · 43% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Frizzled-5	protein	119	44% helix, 8% strand	Q13467
B	Frizzled-5	protein	121	43% helix, 7% strand	Q13467

Ligands and binding sites

PAM · Palmitoleic acid · ligand · 2 copies · chains A, B
FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A, B
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A

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

Pockets

5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	99	0.41	0.77	18	empty
2	94	0.39	0.77	14	empty
3	66	0.36	0.78	20	empty
4	81	0.34	0.74	13	PAM
5	53	0.31	0.76	11	PAM

Interfaces

1 interface between chains.

A–B · 552 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

5URY · Crystal structure of Frizzled 5 CRD in complex with PAM · the same entry in another collection · chain A against A, TM-score 1.00
Q13467 · AlphaFold monomer V2.0 prediction for frizzled-5 (Q13467) · 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 Q13467
Elsewhere: RCSB PDB 5URY · PDBe 5URY · UniProt Q13467

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