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Crystal structure of the human CD4 N-terminal two domain fragment complexed to a class II MHC molecule

Analyse Crystal structure of the human CD4 N-terminal two domain fragment complexed to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1JL4
Type: protein
Length: 556 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: H-2 class II histocompatibility antigen, a-K alpha chain; H-2 class II histocompatibility…
UniProt: P01910, P06343, P02789, P01730
Pockets: 3 · best druggability 0.73

Structure

x-ray diffraction · 4 distinct chains · 14% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	H-2 class II histocompatibility antigen, a-K alpha chain	protein	178	15% helix, 46% strand	P01910
B	H-2 class II histocompatibility antigen, a-K beta chain	protein	185	21% helix, 47% strand	P06343
C	Ovotransferrin	protein	16	0% helix, 13% strand	P02789
D	T-cell surface glycoprotein CD4	protein	177	7% helix, 48% strand	P01730

Pockets

3 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	1161	0.73	0.76	109	empty
2	120	0.42	0.76	23	empty
3	107	0.34	0.73	21	empty

Interfaces

5 interfaces between chains.

A–B · 2420 Å² buried · 43 hydrogen bonds · protein-protein
B–C · 767 Å² buried · 11 hydrogen bonds · protein-protein
A–C · 648 Å² buried · 16 hydrogen bonds · protein-protein
B–D · 366 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 186 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

1JL4 · Crystal structure of the human CD4 N-terminal two domain fragment complexed to a class II… · the same entry in another collection · chain D against D, TM-score 1.00
P01910 · AlphaFold monomer V2.0 prediction for H-2 class II histocompatibility antigen, a-K alpha… · a predicted model of the same protein · chain A against A, TM-score 0.97
P01730 · AlphaFold monomer V2.0 prediction for T-cell surface glycoprotein CD4 (P01730) · a predicted model of the same protein · chain D against A, TM-score 0.97
P06343 · AlphaFold monomer V2.0 prediction for H-2 class II histocompatibility antigen, a-K beta… · a predicted model of the same protein · chain B against A, TM-score 0.96
P02789 · AlphaFold monomer V2.0 prediction for ovotransferrin (P02789) · a predicted model of the same protein · chain C against A, TM-score 0.22

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 P01910
Every structure of UniProt P06343
Every structure of UniProt P02789
Every structure of UniProt P01730
Elsewhere: RCSB PDB 1JL4 · PDBe 1JL4 · UniProt P01910 · UniProt P06343 · UniProt P02789 · UniProt P01730

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