MolNFT v1 · #13525 · protein

Crystal structure of H-2KB bound to the DEV8 peptide

1LEG · H-2 class I histocompatibility antigen, K-B alpha chain: “Crystal structure of H-2KB bound to the DEV8 peptide”. X-ray diffraction, 3 ligands (NAG, FUC, PO4), 5 pockets (best druggability 0.61). MolNFT v1 #13525 on GenesisL1: 3D…

PDB: 1LEG
Type: protein
Length: 381 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: H-2 class I histocompatibility antigen, K-B alpha chain; Beta-2-microglobulin…
UniProt: P01901, P01887, Q62425
Ligands: NAG, FUC, PO4
Pockets: 5 · best druggability 0.61

Structure

x-ray diffraction · 3 distinct chains · 20% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	H-2 class I histocompatibility antigen, K-B alpha chain	protein	274	27% helix, 40% strand	P01901
B	Beta-2-microglobulin	protein	99	0% helix, 53% strand	P01887
P	NADH-ubiquinone oxidoreductase mlrq subunit	protein	8	0% helix, 0% strand	Q62425

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
FUC · alpha-L-fucopyranose · sugar · chains A
PO4 · Phosphate ion · ion · 2 copies · chains A, B

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

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	240	0.61	0.80	34	PO4
2	354	0.56	0.75	36	empty
3	60	0.52	0.87	17	empty
4	102	0.46	0.80	23	empty
5	99	0.45	0.79	17	empty

Interfaces

2 interfaces between chains.

A–B · 1359 Å² buried · 25 hydrogen bonds · protein-protein
A–P · 903 Å² buried · 26 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide, 2 glycan, 1 modified (disulfide, N-glycosylation, oxidation).

Compared structures

1LEG · Crystal Structure of H-2Kb bound to the dEV8 peptide · the same entry in another collection · chain A against A, TM-score 1.00
P01901 · AlphaFold monomer V2.0 prediction for H-2 class I histocompatibility antigen, K-B alpha… · a predicted model of the same protein · chain A 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 B against A, TM-score 0.97
Q62425 · AlphaFold monomer V2.0 prediction for cytochrome C oxidase subunit NDUFA4 (Q62425) · a predicted model of the same protein · chain P against A, TM-score 0.47

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 P01901
Every structure of UniProt P01887
Every structure of UniProt Q62425
Elsewhere: RCSB PDB 1LEG · PDBe 1LEG · UniProt P01901 · UniProt P01887 · UniProt Q62425

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