MolNFT v1 · #120613 · protein

Crystal structure of bony fish MHC class I, peptide and B2M II

5H5Z · MHC class I antigen: “Crystal structure of bony fish MHC class I, peptide and B2M II”. X-ray diffraction, 2 pockets (best druggability 0.66). MolNFT v1 #120613 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5H5Z
Type: protein
Length: 382 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MHC class I antigen; Beta-2-microglobulin; Peptide chain
UniProt: Q65XY8, Q6L7B0
Pockets: 2 · best druggability 0.66

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MHC class I antigen	protein	275	29% helix, 39% strand	Q65XY8
B	Beta-2-microglobulin	protein	98	0% helix, 54% strand	Q6L7B0
C	Peptide chain	protein	9	0% helix, 0% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	519	0.66	0.78	57	empty
2	109	0.47	0.79	25	empty

Interfaces

2 interfaces between chains.

A–B · 1826 Å² buried · 24 hydrogen bonds · protein-protein
A–C · 868 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

5H5Z · Crystal structure of bony fish MHC class I, peptide and B2m II · the same entry in another collection · chain A against A, TM-score 1.00

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 Q65XY8
Every structure of UniProt Q6L7B0
Elsewhere: RCSB PDB 5H5Z · PDBe 5H5Z · UniProt Q65XY8 · UniProt Q6L7B0

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