MolNFT v1 · #100626 · protein

Structure of langerin crd I313 with alpha-meglcnac

4N34 · C-type lectin domain family 4 member K: “Structure of langerin crd I313 with alpha-meglcnac”. X-ray diffraction, 2 ligands (2F8, CA), 7 pockets (best druggability 0.79). MolNFT v1 #100626 on GenesisL1: 3D structure, binding sites…

PDB: 4N34
Type: protein
Length: 514 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: C-type lectin domain family 4 member K
UniProt: Q9UJ71
Ligands: 2F8, CA
Pockets: 7 · best druggability 0.79

Structure

x-ray diffraction · 3 distinct chains · 23% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	C-type lectin domain family 4 member K	protein	128	21% helix, 31% strand	Q9UJ71
C	C-type lectin domain family 4 member K	protein	129	24% helix, 32% strand	Q9UJ71
D	C-type lectin domain family 4 member K	protein	129	24% helix, 31% strand	Q9UJ71

Ligands and binding sites

2F8 · methyl 2-acetamido-2-deoxy-alpha-D-glucopyranoside · ligand · 4 copies · chains A, B, C, D
CA · Calcium ion · metal · 4 copies · chains A, B, C, D

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

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	664	0.79	0.84	87	empty
2	443	0.77	0.86	66	empty
3	175	0.56	0.80	28	empty
4	74	0.35	0.76	17	empty
5	71	0.34	0.76	16	empty

Interfaces

4 interfaces between chains.

B–D · 714 Å² buried · 14 hydrogen bonds · protein-protein
A–C · 690 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 664 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 601 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

4N34 · Structure of langerin CRD I313 with alpha-MeGlcNAc · the same entry in another collection · chain D against D, TM-score 1.00
Q9UJ71 · AlphaFold monomer V2.0 prediction for C-type lectin domain family 4 member K (Q9UJ71) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 Q9UJ71
Elsewhere: RCSB PDB 4N34 · PDBe 4N34 · UniProt Q9UJ71

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