Research workbench

Crystal structure of chicken cCD8aa/pBF2*15:01

Analyse Crystal structure of chicken cCD8aa/pBF2*15:01 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6LHF
Type: protein
Length: 1,196 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.7
Source: Gallus gallus
Molecule: MHC class I; Beta-2-microglobulin; RY0808 peptide; CD8 alpha chain
UniProt: Q9GIP6, P21611, Q6QR64
Pockets: 7 · best druggability 0.87

Structure

x-ray diffraction · resolution 2.7 · 4 distinct chains · 15% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	MHC class I	protein	270	26% helix, 42% strand	Q9GIP6
B, E	Beta-2-microglobulin	protein	96	0% helix, 49% strand	P21611
C, F	RY0808 peptide	protein	8	0% helix, 0% strand	—
G, H, I, J	CD8 alpha chain	protein	112	3% helix, 52% strand	Q6QR64

Pockets

7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1192	0.87	0.88	135	empty
2	1082	0.85	0.86	109	empty
3	662	0.72	0.79	54	empty
4	504	0.68	0.79	41	empty
5	95	0.58	0.87	25	empty

Interfaces

17 interfaces between chains.

A–B · 1549 Å² buried · 17 hydrogen bonds · protein-protein
D–E · 1546 Å² buried · 22 hydrogen bonds · protein-protein
A–C · 1072 Å² buried · 26 hydrogen bonds · protein-protein
D–F · 1048 Å² buried · 26 hydrogen bonds · protein-protein
G–H · 934 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide (disulfide).

Compared structures

6LHF · Crystal structure of chicken CCD8AA/PBF2*15:01 · the same entry in another collection · chain J against J, 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 0.98

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 Q9GIP6
Every structure of UniProt P21611
Every structure of UniProt Q6QR64
Elsewhere: RCSB PDB 6LHF · PDBe 6LHF · UniProt Q9GIP6 · UniProt P21611 · UniProt Q6QR64

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