MolNFT v1 · #122998 · protein

Recognition of the MHC class ib molecule H2-Q10 by the natural killer cell receptor LY49C

5J6G · H-2 class I histocompatibility antigen, Q10 alpha chain: “Recognition of the MHC class ib molecule H2-Q10 by the natural killer cell receptor LY49C”. X-ray diffraction, 13 pockets (best druggability 0.84). MolNFT v1 #122998 on…

PDB: 5J6G
Type: protein
Length: 1,006 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: H-2 class I histocompatibility antigen, Q10 alpha chain; Beta-2-microglobulin…
UniProt: P01898, P01887, Q64329
Pockets: 13 · best druggability 0.84

Structure

x-ray diffraction · 6 distinct chains · 21% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	H-2 class I histocompatibility antigen, Q10 alpha chain	protein	272	27% helix, 39% strand	P01898
B, D	Beta-2-microglobulin	protein	99	0% helix, 52% strand	P01887
C	H-2 class I histocompatibility antigen, Q10 alpha chain	protein	276	26% helix, 38% strand	P01898
E, F	Val-gly-ile-thr-asn-val-asp-leu	protein	8	0% helix, 0% strand	—
G	Killer cell lectin-like receptor 3	protein	122	20% helix, 34% strand	Q64329
H	Killer cell lectin-like receptor 3	protein	122	19% helix, 32% strand	Q64329

Pockets

13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1146	0.84	0.85	86	empty
2	770	0.84	0.87	60	empty
3	269	0.67	0.83	28	empty
4	161	0.57	0.81	27	empty
5	119	0.56	0.83	27	empty

Interfaces

9 interfaces between chains.

C–D · 1313 Å² buried · 25 hydrogen bonds · protein-protein
A–B · 1287 Å² buried · 21 hydrogen bonds · protein-protein
A–G · 973 Å² buried · 11 hydrogen bonds · protein-protein
C–H · 949 Å² buried · 16 hydrogen bonds · protein-protein
C–E · 798 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 disulfide (disulfide).

Compared structures

5J6G · Recognition of the MHC class Ib molecule H2-Q10 by the natural killer cell receptor Ly49C · the same entry in another collection · chain H against H, TM-score 1.00
P01898 · AlphaFold monomer V2.0 prediction for H-2 class I histocompatibility antigen, Q10 alpha… · a predicted model of the same protein · chain C against A, TM-score 0.99
P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · a predicted model of the same protein · chain D 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 P01898
Every structure of UniProt P01887
Every structure of UniProt Q64329
Elsewhere: RCSB PDB 5J6G · PDBe 5J6G · UniProt P01898 · UniProt P01887 · UniProt Q64329

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