MolNFT v1 · #11387 · protein
Crystal structure of the human CD4 N-terminal two domain fragment complexed to a class II MHC molecule
1JL4 · H-2 class II histocompatibility antigen, a-K alpha chain: “Crystal structure of the human CD4 N-terminal two domain fragment complexed to a class II MHC molecule”. X-ray diffraction, 3 pockets (best druggability 0.73). MolNFT v1…
- 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.
| Volume (ų) | 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 Ų buried · 43 hydrogen bonds · protein-protein
- B–C · 767 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 648 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 366 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 186 Ų 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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