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Dimeric form of human LLT1, a ligand for nkr-P1

Analyse Dimeric form of human LLT1, a ligand for nkr-P1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4QKH
Type: protein
Length: 244 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: C-type lectin domain family 2 member D
UniProt: Q9UHP7
Ligands: NAG
Pockets: 2 · best druggability 0.58

Structure

x-ray diffraction · 2 distinct chains · 17% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	C-type lectin domain family 2 member D	protein	123	17% helix, 28% strand	Q9UHP7
B	C-type lectin domain family 2 member D	protein	121	17% helix, 32% strand	Q9UHP7

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B

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

Pockets

2 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	57	0.58	0.91	28	empty
2	50	0.30	0.76	11	empty

Interfaces

1 interface between chains.

A–B · 857 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

4QKH · Dimeric form of human LLT1, a ligand for NKR-P1 · the same entry in another collection · chain A against A, TM-score 1.00
Q9UHP7 · AlphaFold monomer V2.0 prediction for C-type lectin domain family 2 member D (Q9UHP7) · a predicted model of the same protein · chain B against A, TM-score 0.97

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 Q9UHP7
Elsewhere: RCSB PDB 4QKH · PDBe 4QKH · UniProt Q9UHP7

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