Research workbench
Crystal structure of the complex of the MHC class II molecule HLA-DR1(HA peptide 306-318) with the superantigen SEC3
Analyse Crystal structure of the complex of the MHC class II molecule HLA-DR1(HA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JWM
- Type
- protein
- Length
- 612 residues
- Chains
- 4
- 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, P0A0L5
- Pockets
- 7 · best druggability 0.49
Structure
x-ray diffraction · 4 distinct chains · 16% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class II histocompatibility antigen, dr alpha chain | protein | 180 | 14% helix, 47% strand | P01903 |
| B | HLA class II histocompatibility antigen, dr-1 beta chain | protein | 187 | 17% helix, 43% strand | P04229 |
| C | Ha peptide | protein | 13 | 0% helix, 15% strand | — |
| D | Enterotoxin type C-3 | protein | 232 | 19% helix, 33% strand | P0A0L5 |
Pockets
7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 244 | 0.49 | 0.74 | 27 | empty |
| 2 | 166 | 0.47 | 0.76 | 24 | empty |
| 3 | 129 | 0.46 | 0.78 | 17 | empty |
| 4 | 52 | 0.32 | 0.78 | 15 | empty |
| 5 | 50 | 0.32 | 0.77 | 11 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2588 Ų buried · 43 hydrogen bonds · protein-protein
- A–C · 705 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 684 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 684 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1JWM · Crystal Structure of the Complex of the MHC Class II Molecule HLA-DR1(HA peptide 306-318)… · the same entry in another collection · chain A against A, TM-score 1.00
- P0A0L5 · AlphaFold monomer V2.0 prediction for enterotoxin type C-3 (P0A0L5) · a predicted model of the same protein · chain D against A, TM-score 0.99
- 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 0.95
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 P0A0L5
- Elsewhere: RCSB PDB 1JWM · PDBe 1JWM · UniProt P01903 · UniProt P04229 · UniProt P0A0L5
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