MolNFT v1 · #24921 · protein

MHC class I H-2KB heavy chain complexed with beta-2 microglobulin and yeast alpha-glucosidase

1VAD: “MHC class I H-2KB heavy chain complexed with beta-2 microglobulin and yeast alpha-glucosidase”. X-ray diffraction, 5 pockets (best druggability 0.60). MolNFT v1 #24921 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1VAD
Type: protein
Length: 382 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MHC class I H-2KB heavy chain; Beta-2 microglobulin; Yeast alpha-glucosidase
EC: 3.2.1.20
UniProt: P01901, P01887, P38158
Pockets: 5 · best druggability 0.60

Structure

x-ray diffraction · 3 distinct chains · 21% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MHC class I H-2KB heavy chain	protein	274	29% helix, 39% strand	P01901
B	Beta-2 microglobulin	protein	99	0% helix, 53% strand	P01887
P	Yeast alpha-glucosidase (EC 3.2.1.20)	protein	9	0% helix, 0% strand	P38158

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	232	0.60	0.80	31	empty
2	341	0.57	0.76	35	empty
3	73	0.55	0.87	18	empty
4	108	0.47	0.80	22	empty
5	79	0.35	0.76	15	empty

Interfaces

2 interfaces between chains.

A–B · 1377 Å² buried · 26 hydrogen bonds · protein-protein
A–P · 864 Å² buried · 27 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

1VAD · MHC class I H-2KB heavy chain complexed with beta-2 microglobulin and yeast… · the same entry in another collection · chain A against A, 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 0.97
P38158 · AlphaFold monomer V2.0 prediction for alpha-glucosidase MAL32 (P38158) · a predicted model of the same protein · chain P against A, TM-score 0.48

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 P38158
Elsewhere: RCSB PDB 1VAD · PDBe 1VAD · UniProt P01901 · UniProt P01887 · UniProt P38158

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