MolNFT v1 · #22220 · protein

HLA-B*4405 complexed to the dominant self ligand eefgraygf

1SYV · MHC class I antigen: “HLA-B*4405 complexed to the dominant self ligand eefgraygf”. X-ray diffraction, 4 pockets (best druggability 0.68). MolNFT v1 #22220 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1SYV
Type: protein
Length: 384 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MHC class I antigen; Beta-2-microglobulin; Major histocompatibility complex, class II, dr…
UniProt: P30481, P61769, Q9TQB0
Pockets: 4 · best druggability 0.68

Structure

x-ray diffraction · 3 distinct chains · 18% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MHC class I antigen	protein	276	26% helix, 39% strand	P30481
B	Beta-2-microglobulin	protein	99	0% helix, 49% strand	P61769
C	Major histocompatibility complex, class II, dr alpha	protein	9	0% helix, 0% strand	Q9TQB0

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	627	0.68	0.77	55	empty
2	201	0.53	0.78	34	empty
3	96	0.41	0.78	23	empty
4	71	0.38	0.78	15	empty

Interfaces

2 interfaces between chains.

A–B · 1294 Å² buried · 23 hydrogen bonds · protein-protein
A–C · 924 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

1SYV · HLA-B*4405 complexed to the dominant self ligand EEFGRAYGF · the same entry in another collection · chain A against A, TM-score 1.00
P61769 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P61769) · 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 P30481
Every structure of UniProt P61769
Every structure of UniProt Q9TQB0
Elsewhere: RCSB PDB 1SYV · PDBe 1SYV · UniProt P30481 · UniProt P61769 · UniProt Q9TQB0

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