MolNFT v1 · #139661 · protein

Crystal structure of feline MHC class I for 2,1 ångström

5XMF · MHC class I antigen alpha chain: “Crystal structure of feline MHC class I for 2,1 ångström”. X-ray diffraction, 6 pockets (best druggability 0.65). MolNFT v1 #139661 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5XMF
Type: protein
Length: 383 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MHC class I antigen alpha chain; Beta-2-microglobulin; Gag polyprotein
UniProt: C6ZK72, Q5MGS7, P16087
Pockets: 6 · best druggability 0.65

Structure

x-ray diffraction · 3 distinct chains · 20% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MHC class I antigen alpha chain	protein	275	28% helix, 39% strand	C6ZK72
B	Beta-2-microglobulin	protein	99	0% helix, 49% strand	Q5MGS7
C	Gag polyprotein	protein	9	0% helix, 0% strand	P16087

Pockets

6 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	481	0.65	0.77	44	empty
2	99	0.38	0.75	17	empty
3	62	0.35	0.78	16	empty
4	56	0.33	0.77	15	empty
5	79	0.31	0.74	17	empty

Interfaces

2 interfaces between chains.

A–B · 1461 Å² buried · 21 hydrogen bonds · protein-protein
A–C · 938 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

5XMF · Crystal structure of feline MHC class I for 2,1 angstrom · the same entry in another collection · chain A against A, TM-score 1.00
Q5MGS7 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (Q5MGS7) · 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 C6ZK72
Every structure of UniProt Q5MGS7
Every structure of UniProt P16087
Elsewhere: RCSB PDB 5XMF · PDBe 5XMF · UniProt C6ZK72 · UniProt Q5MGS7 · UniProt P16087

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