Research workbench
HLA-DR1 in complex with a synthetic peptide (aaysdqatplllspr)
Analyse HLA-DR1 in complex with a synthetic peptide (aaysdqatplllspr) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1T5W
- Type
- protein
- Length
- 765 residues
- Chains
- 6
- 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
- Pockets
- 11 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 15% helix, 45% 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, E | HLA class II histocompatibility antigen, DRB1-1 beta chain | protein | 190 | 17% helix, 45% strand | P04229 |
| C, F | 15-mer peptide fragment of regulatory protein MIG1 | protein | 13 | 0% helix, 8% strand | P27705 |
| D | HLA class II histocompatibility antigen, dr alpha chain | protein | 179 | 15% helix, 47% strand | P01903 |
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 547 | 0.70 | 0.79 | 61 | empty |
| 2 | 157 | 0.53 | 0.80 | 26 | empty |
| 3 | 144 | 0.53 | 0.80 | 28 | empty |
| 4 | 121 | 0.50 | 0.80 | 23 | empty |
| 5 | 175 | 0.47 | 0.76 | 32 | empty |
Interfaces
10 interfaces between chains.
- D–E · 2579 Ų buried · 47 hydrogen bonds · protein-protein
- A–B · 2562 Ų buried · 45 hydrogen bonds · protein-protein
- E–F · 683 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 681 Ų buried · 10 hydrogen bonds · protein-protein
- D–F · 644 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1T5W · HLA-DR1 in complex with a synthetic peptide (AAYSDQATPLLLSPR) · the same entry in another collection · chain F against F, TM-score 1.00
- 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 0.34
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
- Elsewhere: RCSB PDB 1T5W · PDBe 1T5W · UniProt P01903 · UniProt P04229 · UniProt P27705
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