MolNFT v1 · #186556 · protein

Cryo-EM structure of xenopus patched-1 in nanodisc

7RHR: “Cryo-EM structure of xenopus patched-1 in nanodisc”. Electron microscopy, 2 ligands (CLR, NAG), 9 pockets (best druggability 0.90). MolNFT v1 #186556 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7RHR
Type: protein
Length: 974 residues
Chains: 1
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Patched-1
UniProt: Q98SW6
Ligands: CLR, NAG
Pockets: 9 · best druggability 0.90

Structure

electron microscopy · 1 distinct chain · 56% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Patched-1	protein	974	56% helix, 8% strand	Q98SW6

Ligands and binding sites

CLR · Cholesterol · ligand · 3 copies · chains A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A

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

Pockets

9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1128	0.90	0.91	127	CLR
2	284	0.76	0.88	34	empty
3	218	0.57	0.79	27	empty
4	178	0.52	0.78	19	empty
5	141	0.42	0.74	18	CLR

Modifications

Observed in the structure: 3 disulfide, 3 glycan (disulfide, N-glycosylation).

Compared structures

7RHR · Cryo-EM structure of Xenopus Patched-1 in nanodisc · the same entry in another collection · chain A against A, TM-score 1.00

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 Q98SW6
Elsewhere: RCSB PDB 7RHR · PDBe 7RHR · UniProt Q98SW6

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