MolNFT v1 · #117316 · protein

Structure of ligand binding region of uparap at pH 5.3

5E4L · C-type mannose receptor 2: “Structure of ligand binding region of uparap at pH 5.3”. X-ray diffraction, 2 ligands (NAG, CA), 11 pockets (best druggability 0.56). MolNFT v1 #117316 on GenesisL1: 3D structure, binding sites and…

PDB: 5E4L
Type: protein
Length: 814 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: C-type mannose receptor 2
UniProt: Q9UBG0
Ligands: NAG, CA
Pockets: 11 · best druggability 0.56

Structure

x-ray diffraction · 2 distinct chains · 13% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	C-type mannose receptor 2	protein	428	15% helix, 29% strand	Q9UBG0
B	C-type mannose receptor 2	protein	386	10% helix, 28% strand	Q9UBG0

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
CA · Calcium ion · metal · 6 copies · chains A, B

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

Pockets

11 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	411	0.56	0.74	45	empty
2	164	0.46	0.76	21	empty
3	129	0.46	0.78	21	empty
4	154	0.46	0.76	26	empty
5	160	0.44	0.75	31	empty

Interfaces

1 interface between chains.

A–B · 613 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 18 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

5E4L · Structure of ligand binding region of uPARAP at pH 5.3 · 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 5E4L · PDBe 5E4L · UniProt Q9UBG0

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