Research workbench
Crystal structure of an immune complex
Analyse Crystal structure of an immune complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MAY
- Type
- protein
- Length
- 808 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MHC class II HLA-dq-alpha chain; MHC class II antigen; HY.1B11 TCR alpha chain; UL15…
- UniProt
- Q30066, Q67AJ6
- Ligands
- SO4
- Pockets
- 13 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 10% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | MHC class II HLA-dq-alpha chain | protein | 181 | 14% helix, 44% strand | Q30066 |
| B | MHC class II antigen | protein | 181 | 21% helix, 46% strand | Q67AJ6 |
| C | HY.1B11 TCR alpha chain | protein | 191 | 2% helix, 49% strand | — |
| D | UL15 peptide-HY.1B11 TCR beta chain, chimeric construct | protein | 255 | 6% helix, 47% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 985 | 0.73 | 0.76 | 75 | empty |
| 2 | 154 | 0.62 | 0.85 | 32 | SO4 |
| 3 | 82 | 0.47 | 0.82 | 27 | empty |
| 4 | 130 | 0.46 | 0.78 | 25 | empty |
| 5 | 172 | 0.45 | 0.75 | 25 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2701 Ų buried · 46 hydrogen bonds · protein-protein
- C–D · 2280 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 903 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 786 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 165 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4MAY · Crystal structure of an immune complex · the same entry in another collection · chain A against A, TM-score 1.00
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 Q30066
- Every structure of UniProt Q67AJ6
- Elsewhere: RCSB PDB 4MAY · PDBe 4MAY · UniProt Q30066 · UniProt Q67AJ6
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