MolNFT v1 · #120716 · protein

Crystal structure of swine MHC classi for 1.48 ångströms

5H94 · MHC class I antigen: “Crystal structure of swine MHC classi for 1.48 ångströms”. X-ray diffraction, 8 pockets (best druggability 0.80). MolNFT v1 #120716 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5H94
Type: protein
Length: 762 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MHC class I antigen; Beta-2-microglobulin; Nonapeptide from influenza a virus ha protein
UniProt: Q07717
Pockets: 8 · best druggability 0.80

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	MHC class I antigen	protein	275	29% helix, 41% strand	—
B, E	Beta-2-microglobulin	protein	97	0% helix, 51% strand	Q07717
C, F	Nonapeptide from influenza a virus ha protein	protein	9	0% helix, 0% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	973	0.80	0.81	87	empty
2	562	0.69	0.79	60	empty
3	209	0.67	0.85	37	empty
4	365	0.58	0.76	41	empty
5	163	0.50	0.78	28	empty

Interfaces

8 interfaces between chains.

A–B · 1342 Å² buried · 24 hydrogen bonds · protein-protein
D–E · 1326 Å² buried · 26 hydrogen bonds · protein-protein
A–C · 903 Å² buried · 21 hydrogen bonds · protein-protein
D–F · 854 Å² buried · 17 hydrogen bonds · protein-protein
A–D · 467 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

5H94 · Crystal structure of Swine MHC CLASSI for 1.48 angstroms · the same entry in another collection · chain F against F, TM-score 1.00
Q07717 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (Q07717) · a predicted model of the same protein · chain B 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 Q07717
Elsewhere: RCSB PDB 5H94 · PDBe 5H94 · UniProt Q07717

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