MolNFT v1 · #117315 · protein

Structure of ligand binding region of uparap at pH 7.4

5E4K · C-type mannose receptor 2: “Structure of ligand binding region of uparap at pH 7.4”. X-ray diffraction, 3 ligands (NAG, CA, NA), 4 pockets (best druggability 0.61). MolNFT v1 #117315 on GenesisL1: 3D structure, binding sites and…

PDB: 5E4K
Type: protein
Length: 424 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: C-type mannose receptor 2
UniProt: Q9UBG0
Ligands: NAG, CA, NA
Pockets: 4 · best druggability 0.61

Structure

x-ray diffraction · 1 distinct chain · 14% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	C-type mannose receptor 2	protein	424	14% helix, 34% strand	Q9UBG0

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
CA · Calcium ion · metal · 2 copies · chains A
NA · Sodium ion · metal · chains A
1PE · Pentaethylene glycol · additive · chains A
PE5 · 3,6,9,12,15,18,21,24-octaoxahexacosan-1-ol · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	322	0.61	0.78	30	empty
2	86	0.41	0.78	19	empty
3	109	0.40	0.76	26	empty
4	70	0.32	0.75	15	empty

Modifications

Observed in the structure: 11 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

5E4K · Structure of ligand binding region of uPARAP at pH 7.4 · the same entry in another collection · chain A against A, TM-score 1.00
Q9UBG0 · AlphaFold monomer V2.0 prediction for C-type mannose receptor 2 (Q9UBG0) · 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 Q9UBG0
Elsewhere: RCSB PDB 5E4K · PDBe 5E4K · UniProt Q9UBG0

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