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Crystal structure of MHC-I like protein

Analyse Crystal structure of MHC-I like protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6BMH
Type: protein
Length: 1,484 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Antigen-presenting glycoprotein CD1D2; Beta-2-microglobulin
UniProt: P11610, P01887
Ligands: F61, NAG
Pockets: 19 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 19% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G	Antigen-presenting glycoprotein CD1D2	protein	273	26% helix, 42% strand	P11610
B, D, F, H	Beta-2-microglobulin	protein	98	0% helix, 48% strand	P01887

Ligands and binding sites

F61 · N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]undecanamide · ligand · 4 copies · chains A, C, E, G
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A, C, E, G, H

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

Pockets

19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	392	0.81	0.89	52	F61
2	397	0.80	0.88	44	F61
3	382	0.80	0.88	47	F61
4	445	0.79	0.86	57	F61
5	551	0.67	0.77	69	empty

Interfaces

9 interfaces between chains.

G–H · 1257 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 1255 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 1239 Å² buried · 11 hydrogen bonds · protein-protein
E–F · 1230 Å² buried · 11 hydrogen bonds · protein-protein
E–H · 572 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 glycan, 8 disulfide, 1 covalent (N-glycosylation, disulfide, covalent ligand).

Compared structures

6BMH · Crystal structure of MHC-I like protein · the same entry in another collection · chain H against H, TM-score 1.00
P11610 · AlphaFold monomer V2.0 prediction for antigen-presenting glycoprotein CD1D2 (P11610) · a predicted model of the same protein · chain E against A, TM-score 0.99

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 P11610
Every structure of UniProt P01887
Elsewhere: RCSB PDB 6BMH · PDBe 6BMH · UniProt P11610 · UniProt P01887

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