Research workbench
HLA-DR1 in complex with a synthetic peptide (aaysdqatplllspr) and the superantigen SEC3-3B2
Analyse HLA-DR1 in complex with a synthetic peptide (aaysdqatplllspr) and the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1T5X
- 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, P27705, P0A0L5
- Pockets
- 6 · best druggability 0.49
Structure
x-ray diffraction · 4 distinct chains · 17% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class II histocompatibility antigen, dr alpha chain | protein | 179 | 15% helix, 47% strand | P01903 |
| B | HLA class II histocompatibility antigen, DRB1-1 beta chain | protein | 190 | 19% helix, 44% strand | P04229 |
| C | 15-mer peptide fragment of regulatory protein MIG1 | protein | 13 | 0% helix, 8% strand | P27705 |
| D | Enterotoxin type C-3 | protein | 230 | 19% helix, 33% strand | P0A0L5 |
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 209 | 0.49 | 0.75 | 23 | empty |
| 2 | 158 | 0.48 | 0.77 | 24 | empty |
| 3 | 117 | 0.37 | 0.74 | 27 | empty |
| 4 | 67 | 0.37 | 0.78 | 13 | empty |
| 5 | 60 | 0.26 | 0.72 | 14 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2518 Ų buried · 42 hydrogen bonds · protein-protein
- B–C · 659 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 647 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 640 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1T5X · HLA-DR1 in complex with a synthetic peptide (AAYSDQATPLLLSPR) and the superantigen… · 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 0.96
- P27705 · AlphaFold monomer V2.0 prediction for regulatory protein MIG1 (P27705) · a predicted model of the same protein · chain C against A, TM-score 0.33
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 P27705
- Every structure of UniProt P0A0L5
- Elsewhere: RCSB PDB 1T5X · PDBe 1T5X · UniProt P01903 · UniProt P04229 · UniProt P27705 · UniProt P0A0L5
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