MolNFT v1 · #186783 · protein

Cryo-EM structure of murine dispatched nnn mutant

7RPJ · Protein dispatched homolog 1: “Cryo-EM structure of murine dispatched nnn mutant”. Electron microscopy, 2 ligands (Y01, NAG), 13 pockets (best druggability 0.65). MolNFT v1 #186783 on GenesisL1: 3D structure, binding sites and…

PDB: 7RPJ
Type: protein
Length: 926 residues
Chains: 1
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein dispatched homolog 1
UniProt: Q3TDN0
Ligands: Y01, NAG
Pockets: 13 · best druggability 0.65

Structure

electron microscopy · 1 distinct chain · 60% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein dispatched homolog 1	protein	926	60% helix, 7% strand	Q3TDN0

Ligands and binding sites

Y01 · Cholesterol hemisuccinate · ligand · 14 copies · chains A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A

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

Pockets

13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	236	0.65	0.83	35	empty
2	134	0.63	0.86	23	empty
3	170	0.61	0.83	26	empty
4	363	0.59	0.76	35	Y01
5	321	0.57	0.76	41	empty

Modifications

Observed in the structure: 9 disulfide, 5 glycan (disulfide, N-glycosylation).

Compared structures

7RPJ · Cryo-EM structure of murine Dispatched NNN mutant · the same entry in another collection · chain A against A, TM-score 1.00
Q3TDN0 · AlphaFold monomer V2.0 prediction for protein dispatched homolog 1 (Q3TDN0) · 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 Q3TDN0
Elsewhere: RCSB PDB 7RPJ · PDBe 7RPJ · UniProt Q3TDN0

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