MolNFT v1 · #157894 · protein

Designed repeat protein in complex with FZ8

6NDZ · Frizzled-8: “Designed repeat protein in complex with FZ8”. X-ray diffraction, 7 pockets (best druggability 0.79). MolNFT v1 #157894 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6NDZ
Type: protein
Length: 931 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Frizzled-8; Designed repeat binding protein
UniProt: Q9H461
Pockets: 7 · best druggability 0.79

Structure

x-ray diffraction · 4 distinct chains · 49% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Frizzled-8	protein	122	39% helix, 6% strand	Q9H461
B, D	Designed repeat binding protein	protein	190	55% helix, 0% strand	—
C, E	Frizzled-8	protein	120	39% helix, 6% strand	Q9H461
F	Designed repeat binding protein	protein	189	58% helix, 0% strand	—

Ligands and binding sites

MPD · (4S)-2-methyl-2,4-pentanediol · additive · 4 copies · chains A, B
ACT · Acetate ion · additive · 4 copies · chains A, C, D
ACY · Acetic acid · additive · 2 copies · chains A, C, F

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

Pockets

7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1001	0.79	0.81	89	MPD, ACY
2	609	0.71	0.79	46	ACT
3	199	0.50	0.76	32	empty
4	109	0.43	0.77	17	empty
5	116	0.41	0.76	17	empty

Interfaces

7 interfaces between chains.

C–D · 1291 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 1261 Å² buried · 11 hydrogen bonds · protein-protein
E–F · 1252 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 449 Å² buried · 9 hydrogen bonds · protein-protein
A–D · 269 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 15 disulfide (disulfide).

Compared structures

6NDZ · Designed repeat protein in complex with Fz8 · the same entry in another collection · chain F against F, TM-score 1.00
Q9H461 · AlphaFold monomer V2.0 prediction for frizzled-8 (Q9H461) · a predicted model of the same protein · chain C 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 Q9H461
Elsewhere: RCSB PDB 6NDZ · PDBe 6NDZ · UniProt Q9H461

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