MolNFT v1 · #152211 · protein

Structure of human NKP46 in complex with antibody NKP46-1 and NKP46-4

6IAP · Natural cytotoxicity triggering receptor 1: “Structure of human NKP46 in complex with antibody NKP46-1 and NKP46-4”. X-ray diffraction, 11 pockets (best druggability 0.62). MolNFT v1 #152211 on GenesisL1: 3D structure, binding sites…

PDB: 6IAP
Type: protein
Length: 1,041 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Natural cytotoxicity triggering receptor 1; Fab NKP46-4 light chain; Fab NKP46-4 heavy…
UniProt: O76036
Pockets: 11 · best druggability 0.62

Structure

x-ray diffraction · 5 distinct chains · 5% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Natural cytotoxicity triggering receptor 1	protein	182	2% helix, 49% strand	O76036
D	Fab NKP46-4 light chain	protein	211	6% helix, 50% strand	—
E	Fab NKP46-4 heavy chain	protein	217	4% helix, 53% strand	—
H	Fab NKP46-1 heavy chain	protein	220	7% helix, 48% strand	—
L	Fab NKP46-1 light chain	protein	211	7% helix, 49% strand	—

Pockets

11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	589	0.62	0.74	62	empty
2	380	0.57	0.75	46	empty
3	89	0.50	0.82	18	empty
4	84	0.41	0.78	14	empty
5	68	0.35	0.76	19	empty

Interfaces

6 interfaces between chains.

H–L · 1959 Å² buried · 16 hydrogen bonds · protein-protein
D–E · 1796 Å² buried · 9 hydrogen bonds · protein-protein
A–H · 623 Å² buried · 12 hydrogen bonds · protein-protein
A–E · 493 Å² buried · 5 hydrogen bonds · protein-protein
A–D · 382 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide (disulfide).

Compared structures

6IAP · structure of human NKp46 in complex with antibody NKp46-1 and NKp46-4 · the same entry in another collection · chain A against A, TM-score 1.00
O76036 · AlphaFold monomer V2.0 prediction for natural cytotoxicity triggering receptor 1 (O76036) · a predicted model of the same protein · chain A against A, TM-score 0.94

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 O76036
Elsewhere: RCSB PDB 6IAP · PDBe 6IAP · UniProt O76036

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