Research workbench
Structural basis of chronic beryllium disease: bridging the gap between allergic hypersensitivity and auto immunity
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
- 4P4K
- Type
- protein
- Length
- 1,644 residues
- Chains
- 8
- 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, NA, 0BE
- Pockets
- 18 · best druggability 0.66
Structure
x-ray diffraction · 7 distinct chains · 9% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HLA class II histocompatibility antigen, dp alpha 1 chain | protein | 178 | 15% helix, 46% strand | P20036 |
| B, F | MIM2 PEPTIDE,HLA class II histocompatibility antigen, dp beta 1 chain | protein | 199 | 15% helix, 43% strand | P04440 |
| C | HTCRAV22 alpha chain | protein | 204 | 5% helix, 46% strand | — |
| D | HTCRAV22 beta chain | protein | 241 | 6% helix, 51% strand | — |
| E | HLA class II histocompatibility antigen, dp alpha 1 chain | protein | 181 | 14% helix, 45% strand | P20036 |
| G | HTCRAV22 alpha chain | protein | 203 | 5% helix, 44% strand | — |
| H | HTCRAV22 beta chain | protein | 239 | 6% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B, E
- NA · Sodium ion · metal · 2 copies · chains B, F
- 0BE · Beryllium · metal · 2 copies · chains B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 424 | 0.66 | 0.79 | 61 | empty |
| 2 | 735 | 0.65 | 0.74 | 75 | empty |
| 3 | 629 | 0.62 | 0.74 | 72 | empty |
| 4 | 237 | 0.57 | 0.78 | 26 | empty |
| 5 | 239 | 0.50 | 0.74 | 36 | empty |
Interfaces
16 interfaces between chains.
- E–F · 3224 Ų buried · 63 hydrogen bonds · protein-protein
- A–B · 3118 Ų buried · 61 hydrogen bonds · protein-protein
- C–D · 2023 Ų buried · 26 hydrogen bonds · protein-protein
- G–H · 2003 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 592 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 4P4K · Structural Basis of Chronic Beryllium Disease: Bridging the Gap Between allergic… · the same entry in another collection · chain H against H, 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 0.96
- 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 0.77
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 4P4K · PDBe 4P4K · UniProt P20036 · UniProt P04440
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