Research workbench
HLA-DR1 complexed with a 13 residue HIV capsid peptide
Analyse HLA-DR1 complexed with a 13 residue HIV capsid peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SJH
- 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, P12495, P0A0L5
- Pockets
- 5 · best druggability 0.51
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 | 13% helix, 46% strand | P01903 |
| B | HLA class II histocompatibility antigen, DRB1-1 beta chain | protein | 190 | 19% helix, 44% strand | P04229 |
| C | Gag polyprotein | protein | 13 | 0% helix, 8% strand | P12495 |
| D | Enterotoxin type C-3 | protein | 230 | 20% helix, 34% strand | P0A0L5 |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 267 | 0.51 | 0.74 | 36 | empty |
| 2 | 94 | 0.50 | 0.82 | 22 | empty |
| 3 | 171 | 0.46 | 0.75 | 20 | empty |
| 4 | 104 | 0.36 | 0.74 | 17 | empty |
| 5 | 60 | 0.30 | 0.74 | 13 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2515 Ų buried · 47 hydrogen bonds · protein-protein
- A–D · 622 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 600 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 578 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1SJH · HLA-DR1 complexed with a 13 residue HIV capsid peptide · 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
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 P12495
- Every structure of UniProt P0A0L5
- Elsewhere: RCSB PDB 1SJH · PDBe 1SJH · UniProt P01903 · UniProt P04229 · UniProt P12495 · UniProt P0A0L5
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