Research workbench
Crystal structure of HLA-DR1 with CLIP106-120, flipped peptide orientation
Analyse Crystal structure of HLA-DR1 with CLIP106-120, flipped peptide orientation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PGC
- Type
- protein
- Length
- 749 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 0.75
Structure
x-ray diffraction · 5 distinct chains · 16% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class II histocompatibility antigen, dr alpha chain | protein | 177 | 14% helix, 47% strand | P01903 |
| B | HLA class II histocompatibility antigen, DRB1-1 beta chain | protein | 184 | 17% helix, 45% strand | P04229 |
| C, F | HLA class II histocompatibility antigen gamma chain | protein | 15 | 0% helix, 13% strand | P04233 |
| D | HLA class II histocompatibility antigen, dr alpha chain | protein | 178 | 14% helix, 48% strand | P01903 |
| E | HLA class II histocompatibility antigen, DRB1-1 beta chain | protein | 180 | 19% helix, 46% strand | P04229 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 1114 | 0.75 | 0.77 | 93 | empty |
| 2 | 459 | 0.70 | 0.81 | 36 | empty |
| 3 | 325 | 0.52 | 0.73 | 38 | empty |
| 4 | 91 | 0.33 | 0.73 | 15 | empty |
| 5 | 71 | 0.32 | 0.74 | 16 | empty |
Interfaces
8 interfaces between chains.
- D–E · 2577 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 2523 Ų buried · 43 hydrogen bonds · protein-protein
- D–F · 700 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 672 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 668 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3PGC · Crystal Structure of HLA-DR1 with CLIP106-120, flipped 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 D against A, TM-score 0.96
- 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 0.27
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 3PGC · PDBe 3PGC · UniProt P01903 · UniProt P04229 · UniProt P04233
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