Research workbench
Structural basis of chronic beryllium disease: bridging the gap between allergic hypersensitivity and autoimmunity
Analyse Structural basis of chronic beryllium disease: bridging the gap between… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4P4R
- Type
- protein
- Length
- 754 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HLA class II histocompatibility antigen, dp alpha 1 chain; MIM2 PEPTIDE,HLA class II…
- UniProt
- P20036, P04440
- Ligands
- NAG
- Pockets
- 8 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | HLA class II histocompatibility antigen, dp alpha 1 chain | protein | 178 | 15% helix, 45% strand | P20036 |
| B, D | MIM2 PEPTIDE,HLA class II histocompatibility antigen, dp beta 1 chain | protein | 199 | 17% helix, 43% strand | P04440 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 498 | 0.64 | 0.77 | 51 | empty |
| 2 | 678 | 0.63 | 0.73 | 64 | empty |
| 3 | 396 | 0.59 | 0.76 | 36 | empty |
| 4 | 178 | 0.50 | 0.77 | 27 | empty |
| 5 | 78 | 0.38 | 0.77 | 26 | empty |
Interfaces
6 interfaces between chains.
- C–D · 3166 Ų buried · 66 hydrogen bonds · protein-protein
- A–B · 3151 Ų buried · 63 hydrogen bonds · protein-protein
- A–D · 359 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 333 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 242 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 4P4R · Structural Basis of Chronic Beryllium Disease: Bridging the Gap Between Allergic… · the same entry in another collection · chain A against A, TM-score 1.00
- P20036 · AlphaFold monomer V2.0 prediction for HLA class II histocompatibility antigen, dp alpha 1… · a predicted model of the same protein · chain A against A, TM-score 0.95
- P04440 · AlphaFold monomer V2.0 prediction for HLA class II histocompatibility antigen, dp beta 1… · a predicted model of the same protein · chain B against A, TM-score 0.79
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 P20036
- Every structure of UniProt P04440
- Elsewhere: RCSB PDB 4P4R · PDBe 4P4R · UniProt P20036 · UniProt P04440
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