MolNFT v1 · #160028 · protein

N-terminal 5 domains of igfiir

6P8I · Cation-independent mannose-6-phosphate receptor: “N-terminal 5 domains of igfiir”. X-ray diffraction, 3 ligands (NAG, BMA, MAN), 9 pockets (best druggability 0.79). MolNFT v1 #160028 on GenesisL1: 3D structure, binding sites and…

PDB: 6P8I
Type: protein
Length: 666 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cation-independent mannose-6-phosphate receptor
UniProt: P11717
Ligands: NAG, BMA, MAN
Pockets: 9 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 6% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cation-independent mannose-6-phosphate receptor	protein	666	6% helix, 40% strand	P11717

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
BMA · beta-D-mannopyranose · sugar
MAN · alpha-D-mannopyranose · sugar

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	494	0.79	0.87	69	empty
2	539	0.74	0.82	43	empty
3	140	0.66	0.87	22	empty
4	281	0.58	0.78	49	empty
5	152	0.48	0.77	22	empty

Modifications

Observed in the structure: 14 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

6P8I · N-terminal 5 domains of IGFIIR · the same entry in another collection · chain A against A, TM-score 1.00
P11717 · AlphaFold monomer V2.0 prediction for cation-independent mannose-6-phosphate receptor… · a predicted model of the same protein · chain A against A, TM-score 0.89

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 P11717
Elsewhere: RCSB PDB 6P8I · PDBe 6P8I · UniProt P11717

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