MolNFT v1 · #144238 · protein

Crystal structure of TCR-MHC-like molecule

6BNK · Antigen-presenting glycoprotein CD1D1: “Crystal structure of TCR-MHC-like molecule”. X-ray diffraction, 2 ligands (AGH, NAG), 17 pockets (best druggability 0.85). MolNFT v1 #144238 on GenesisL1: 3D structure, binding sites and…

PDB: 6BNK
Type: protein
Length: 1,622 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Antigen-presenting glycoprotein CD1D1; Beta-2-microglobulin; Nkt VALPHA14 (mouse) - 2C12…
UniProt: A0A0R4J090, P01887
Ligands: AGH, NAG
Pockets: 17 · best druggability 0.85

Structure

x-ray diffraction · 4 distinct chains · 11% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Antigen-presenting glycoprotein CD1D1	protein	272	26% helix, 40% strand	A0A0R4J090
B, F	Beta-2-microglobulin	protein	97	0% helix, 53% strand	P01887
C, G	Nkt VALPHA14 (mouse) - 2C12 TCR - hybrid mouse variable and human constant domains	protein	203	3% helix, 49% strand	—
D, H	Nkt VBETA8.2 (mouse) - 2C12 TCR - hybrid mouse variable and human constant domains	protein	239	6% helix, 49% strand	—

Ligands and binding sites

AGH · N-{(1S,2R,3S)-1-[(alpha-D-galactopyranosyloxy)methyl]-2,3-dihydroxyheptadecyl}hexacosanamide · ligand · 2 copies · chains A, C, E, G
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, E

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

Pockets

17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	768	0.85	0.88	77	AGH
2	816	0.85	0.87	74	AGH
3	572	0.70	0.79	62	empty
4	771	0.66	0.74	68	empty
5	288	0.65	0.82	33	empty

Interfaces

11 interfaces between chains.

G–H · 2127 Å² buried · 24 hydrogen bonds · protein-protein
C–D · 2117 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 1174 Å² buried · 13 hydrogen bonds · protein-protein
E–F · 1172 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 480 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide, 6 glycan (disulfide, N-glycosylation).

Compared structures

6BNK · Crystal structure of TCR-MHC-like molecule · the same entry in another collection · chain H against H, TM-score 1.00
P01887 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P01887) · 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 A0A0R4J090
Every structure of UniProt P01887
Elsewhere: RCSB PDB 6BNK · PDBe 6BNK · UniProt A0A0R4J090 · UniProt P01887

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