Research workbench
Crystal structure of HLA-DR2 (DRA*0101,DRB1*1501) complexed with a peptide from human myelin basic protein
Analyse Crystal structure of HLA-DR2 (DRA*0101,DRB1*1501) complexed with a peptide from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1BX2
- Type
- protein
- Length
- 768 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (HLA-DR2)
- UniProt
- P01903, P04229
- Ligands
- NAG
- Pockets
- 14 · best druggability 0.66
Structure
x-ray diffraction · 5 distinct chains · 16% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Protein (HLA-DR2) | protein | 180 | 14% helix, 45% strand | P01903 |
| B | Protein (HLA-DR2) | protein | 191 | 18% helix, 46% strand | P04229 |
| C | Protein (HLA-DR2) | protein | 14 | 0% helix, 7% strand | — |
| E | Protein (HLA-DR2) | protein | 189 | 20% helix, 46% strand | P04229 |
| F | Protein (HLA-DR2) | protein | 14 | 0% helix, 7% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 411 | 0.66 | 0.79 | 60 | empty |
| 2 | 162 | 0.54 | 0.80 | 20 | empty |
| 3 | 63 | 0.53 | 0.87 | 21 | empty |
| 4 | 165 | 0.51 | 0.78 | 32 | empty |
| 5 | 188 | 0.50 | 0.76 | 22 | empty |
Interfaces
10 interfaces between chains.
- A–B · 2620 Ų buried · 37 hydrogen bonds · protein-protein
- D–E · 2586 Ų buried · 39 hydrogen bonds · protein-protein
- D–F · 638 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 605 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 574 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 1BX2 · Crystal structure of HLA-DR2 (DRA*0101,DRB1*1501) complexed with a peptide from human… · 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 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
- Elsewhere: RCSB PDB 1BX2 · PDBe 1BX2 · UniProt P01903 · UniProt P04229
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