Research workbench
Structural basis of chronic beryllium disease: bridging the gap between allergy and autoimmunity
Analyse Structural basis of chronic beryllium disease: bridging the gap between allergy… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4P5K
- Type
- protein
- Length
- 758 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; RAS PEPTIDE,HLA class II…
- UniProt
- P20036, Q5EP54
- Pockets
- 9 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | HLA class II histocompatibility antigen, dp alpha 1 chain | protein | 181 | 14% helix, 45% strand | P20036 |
| B, E | RAS PEPTIDE,HLA class II histocompatibility antigen, dp beta 1 chain | protein | 198 | 16% helix, 42% strand | Q5EP54 |
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 324 | 0.53 | 0.74 | 46 | empty |
| 2 | 182 | 0.46 | 0.75 | 20 | empty |
| 3 | 164 | 0.45 | 0.76 | 28 | empty |
| 4 | 122 | 0.42 | 0.76 | 29 | empty |
| 5 | 141 | 0.38 | 0.73 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3298 Ų buried · 57 hydrogen bonds · protein-protein
- D–E · 3248 Ų buried · 60 hydrogen bonds · protein-protein
- A–D · 334 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4P5K · Structural Basis of Chronic Beryllium Disease: Bridging the Gap Between Allergy and… · 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
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 Q5EP54
- Elsewhere: RCSB PDB 4P5K · PDBe 4P5K · UniProt P20036 · UniProt Q5EP54
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.