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Crystal structure of the CD8 alpha BETA/H-2DD complex

Analyse Crystal structure of the CD8 alpha BETA/H-2DD complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3DMM
Type: protein
Length: 625 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: H-2 class I histocompatibility antigen, D-D alpha chain; Beta-2 microglobulin; Synthetic…
UniProt: P01900, Q91XJ8, P01731, P10300
Pockets: 8 · best druggability 0.72

Structure

x-ray diffraction · 5 distinct chains · 13% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	H-2 class I histocompatibility antigen, D-D alpha chain	protein	274	27% helix, 38% strand	P01900
B	Beta-2 microglobulin	protein	100	0% helix, 47% strand	Q91XJ8
P	Synthetic peptide	protein	10	0% helix, 0% strand	—
C	T-cell surface glycoprotein CD8 alpha chain	protein	118	3% helix, 48% strand	P01731
D	T-cell surface glycoprotein CD8 beta chain	protein	123	2% helix, 49% strand	P10300

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	579	0.72	0.81	58	empty
2	426	0.72	0.83	50	empty
3	101	0.44	0.78	22	empty
4	126	0.41	0.75	21	empty
5	141	0.41	0.74	26	empty

Interfaces

5 interfaces between chains.

A–B · 1384 Å² buried · 14 hydrogen bonds · protein-protein
C–D · 924 Å² buried · 6 hydrogen bonds · protein-protein
A–P · 915 Å² buried · 22 hydrogen bonds · protein-protein
A–C · 529 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 370 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

3DMM · Crystal structure of the CD8 alpha beta/H-2Dd complex · the same entry in another collection · chain D against D, TM-score 1.00
P01900 · AlphaFold monomer V2.0 prediction for H-2 class I histocompatibility antigen, D-D alpha… · a predicted model of the same protein · chain A against A, TM-score 0.97
P01731 · AlphaFold monomer V2.0 prediction for T-cell surface glycoprotein CD8 alpha chain (P01731) · a predicted model of the same protein · chain C against A, TM-score 0.93
P10300 · AlphaFold monomer V2.0 prediction for T-cell surface glycoprotein CD8 beta chain (P10300) · a predicted model of the same protein · chain D against A, TM-score 0.93

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 P01900
Every structure of UniProt Q91XJ8
Every structure of UniProt P01731
Every structure of UniProt P10300
Elsewhere: RCSB PDB 3DMM · PDBe 3DMM · UniProt P01900 · UniProt Q91XJ8 · UniProt P01731 · UniProt P10300

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