Research workbench

Structure of the chicken MHC class I molecule BF2*0401

Analyse Structure of the chicken MHC class I molecule BF2*0401 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4E0R
Type: protein
Length: 754 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MHC class I alpha chain 2; Beta-2 microglobulin; 8-meric peptide (FUS/TLS)
UniProt: O46790, P21611, Q6J4Y8
Pockets: 8 · best druggability 0.76

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	MHC class I alpha chain 2	protein	272	28% helix, 39% strand	O46790
B, E	Beta-2 microglobulin	protein	97	0% helix, 53% strand	P21611
C, F	8-meric peptide (FUS/TLS)	protein	8	0% helix, 0% strand	Q6J4Y8

Pockets

8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	75	0.76	0.98	21	empty
2	508	0.68	0.79	51	empty
3	488	0.67	0.79	53	empty
4	295	0.64	0.81	41	empty
5	105	0.53	0.83	28	empty

Interfaces

8 interfaces between chains.

D–E · 1505 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 1502 Å² buried · 21 hydrogen bonds · protein-protein
A–C · 922 Å² buried · 26 hydrogen bonds · protein-protein
D–F · 887 Å² buried · 29 hydrogen bonds · protein-protein
A–D · 788 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

4E0R · Structure of the chicken MHC class I molecule BF2*0401 · the same entry in another collection · chain F against F, TM-score 1.00
P21611 · AlphaFold monomer V2.0 prediction for beta-2-microglobulin (P21611) · a predicted model of the same protein · chain E against A, TM-score 0.96

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 O46790
Every structure of UniProt P21611
Every structure of UniProt Q6J4Y8
Elsewhere: RCSB PDB 4E0R · PDBe 4E0R · UniProt O46790 · UniProt P21611 · UniProt Q6J4Y8

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