MolNFT v1 · #78296 · protein
Crystal structure of CD4 mutant bound to HLA-DR1
3S4S · HLA class II histocompatibility antigen, dr alpha chain: “Crystal structure of CD4 mutant bound to HLA-DR1”. X-ray diffraction, 11 pockets (best druggability 0.67). MolNFT v1 #78296 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3S4S
- Type
- protein
- Length
- 1,106 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class II histocompatibility antigen, dr alpha chain; HLA class II histocompatibility…
- UniProt
- P01903, P04229, Q9YS52, P01730
- Pockets
- 11 · best druggability 0.67
Structure
x-ray diffraction · 7 distinct chains · 12% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class II histocompatibility antigen, dr alpha chain | protein | 178 | 14% helix, 47% strand | P01903 |
| B | HLA class II histocompatibility antigen, DRB1-1 beta chain | protein | 186 | 18% helix, 46% strand | P04229 |
| C, F | Hemagglutinin peptide | protein | 13 | 0% helix, 8% strand | Q9YS52 |
| G | T-cell surface glycoprotein CD4 | protein | 176 | 7% helix, 48% strand | P01730 |
| D | HLA class II histocompatibility antigen, dr alpha chain | protein | 180 | 14% helix, 47% strand | P01903 |
| E | HLA class II histocompatibility antigen, DRB1-1 beta chain | protein | 185 | 17% helix, 45% strand | P04229 |
| H | T-cell surface glycoprotein CD4 | protein | 175 | 3% helix, 49% strand | P01730 |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 526 | 0.67 | 0.78 | 56 | GOL |
| 2 | 442 | 0.64 | 0.77 | 40 | empty |
| 3 | 273 | 0.61 | 0.80 | 31 | empty |
| 4 | 285 | 0.60 | 0.78 | 30 | empty |
| 5 | 335 | 0.59 | 0.77 | 38 | empty |
Interfaces
13 interfaces between chains.
- D–E · 2692 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 2631 Ų buried · 45 hydrogen bonds · protein-protein
- E–F · 723 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 684 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 656 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 3S4S · Crystal structure of CD4 mutant bound to HLA-DR1 · the same entry in another collection · chain H against H, TM-score 1.00
- P01730 · AlphaFold monomer V2.0 prediction for T-cell surface glycoprotein CD4 (P01730) · a predicted model of the same protein · chain G against A, TM-score 0.98
- P01903 · AlphaFold monomer V2.0 prediction for HLA class II histocompatibility antigen, dr alpha… · a predicted model of the same protein · chain A 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 P01903
- Every structure of UniProt P04229
- Every structure of UniProt Q9YS52
- Every structure of UniProt P01730
- Elsewhere: RCSB PDB 3S4S · PDBe 3S4S · UniProt P01903 · UniProt P04229 · UniProt Q9YS52 · UniProt P01730
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