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Structure of M-6-P/IGFII receptor at pH 4.5

Analyse Structure of M-6-P/IGFII receptor at pH 4.5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6UM1
Type: protein
Length: 2,208 residues
Chains: 1
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cation-independent mannose-6-phosphate receptor
UniProt: P08169
Ligands: NAG, BMA
Pockets: 20 · best druggability 0.79

Structure

electron microscopy · 1 distinct chain · 2% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cation-independent mannose-6-phosphate receptor	protein	2208	2% helix, 32% strand	P08169

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A
BMA · beta-D-mannopyranose · sugar

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

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	895	0.79	0.81	102	empty
2	991	0.78	0.80	108	empty
3	832	0.77	0.80	81	empty
4	426	0.76	0.85	69	empty
5	1000	0.75	0.78	101	empty

Modifications

Observed in the structure: 59 disulfide, 6 glycan (disulfide, N-glycosylation, glycation, glycosylation).

Compared structures

6UM1 · Structure of M-6-P/IGFII Receptor at pH 4.5 · the same entry in another collection · chain A against A, TM-score 1.00
P08169 · 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 0.58

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 P08169
Elsewhere: RCSB PDB 6UM1 · PDBe 6UM1 · UniProt P08169

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