Research workbench
Crystal structure of HLA-DR1 with CLIP106-120, canonical peptide orientation
Analyse Crystal structure of HLA-DR1 with CLIP106-120, canonical peptide orientation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PGD
- Type
- protein
- Length
- 757 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, P04233
- Pockets
- 7 · best druggability 0.62
Structure
x-ray diffraction · 4 distinct chains · 15% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class II histocompatibility antigen, dr alpha chain | protein | 178 | 13% helix, 47% strand | P01903 |
| B, E | HLA class II histocompatibility antigen, DRB1-1 beta chain | protein | 185 | 18% helix, 46% strand | P04229 |
| C, F | HLA class II histocompatibility antigen gamma chain | protein | 15 | 0% helix, 7% strand | P04233 |
| D | HLA class II histocompatibility antigen, dr alpha chain | protein | 179 | 14% helix, 47% strand | P01903 |
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 318 | 0.62 | 0.79 | 21 | empty |
| 2 | 596 | 0.62 | 0.74 | 50 | empty |
| 3 | 499 | 0.58 | 0.73 | 37 | empty |
| 4 | 140 | 0.42 | 0.75 | 25 | empty |
| 5 | 109 | 0.37 | 0.75 | 18 | empty |
Interfaces
9 interfaces between chains.
- D–E · 2630 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 2590 Ų buried · 44 hydrogen bonds · protein-protein
- B–C · 687 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 679 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 606 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3PGD · Crystal Structure of HLA-DR1 with CLIP106-120, canonical peptide orientation · 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 0.97
- P04233 · AlphaFold monomer V2.0 prediction for HLA class II histocompatibility antigen gamma chain… · a predicted model of the same protein · chain C against A, TM-score 0.31
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 P04233
- Elsewhere: RCSB PDB 3PGD · PDBe 3PGD · UniProt P01903 · UniProt P04229 · UniProt P04233
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