Research workbench
F54C HLA-DR1 bound with clip peptide
Analyse F54C HLA-DR1 bound with clip peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QXD
- Type
- protein
- Length
- 762 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
- 8 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | HLA class II histocompatibility antigen, dr alpha chain | protein | 178 | 15% helix, 47% strand | P01903 |
| B, E | HLA class II histocompatibility antigen, DRB1-1 beta chain | protein | 189 | 19% helix, 46% strand | P04229 |
| F, C | HLA class II histocompatibility antigen gamma chain peptide | protein | 14 | 0% helix, 14% strand | P04233 |
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 950 | 0.73 | 0.77 | 96 | empty |
| 2 | 367 | 0.61 | 0.77 | 48 | empty |
| 3 | 198 | 0.55 | 0.79 | 31 | empty |
| 4 | 202 | 0.52 | 0.77 | 24 | empty |
| 5 | 84 | 0.34 | 0.75 | 19 | empty |
Interfaces
10 interfaces between chains.
- A–B · 2480 Ų buried · 43 hydrogen bonds · protein-protein
- D–E · 2477 Ų buried · 51 hydrogen bonds · protein-protein
- D–F · 670 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 659 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 619 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 3QXD · F54C HLA-DR1 bound with CLIP peptide · the same entry in another collection · chain C against C, 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 F 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 3QXD · PDBe 3QXD · UniProt P01903 · UniProt P04229 · UniProt P04233
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