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
- 4P5M
- Type
- protein
- Length
- 1,499 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; PEPTIDE,HLA class II…
- UniProt
- P20036, Q5EP54
- Ligands
- NAG, BMA, NA
- Pockets
- 18 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 18% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | HLA class II histocompatibility antigen, dp alpha 1 chain | protein | 180 | 15% helix, 46% strand | P20036 |
| B, D | PEPTIDE,HLA class II histocompatibility antigen, dp beta 1 chain | protein | 199 | 20% helix, 42% strand | Q5EP54 |
| F | PEPTIDE,HLA class II histocompatibility antigen, dp beta 1 chain | protein | 190 | 18% helix, 45% strand | Q5EP54 |
| H | PEPTIDE,HLA class II histocompatibility antigen, dp beta 1 chain | protein | 191 | 18% helix, 45% strand | Q5EP54 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 19 copies · chains A, B, H, C, D, F, G, E
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains D, B
- NA · Sodium ion · metal · 2 copies · chains A, B, C, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 799 | 0.79 | 0.82 | 65 | empty |
| 2 | 808 | 0.78 | 0.81 | 69 | empty |
| 3 | 1052 | 0.78 | 0.80 | 107 | empty |
| 4 | 1044 | 0.77 | 0.79 | 104 | empty |
| 5 | 70 | 0.70 | 0.96 | 25 | empty |
Interfaces
17 interfaces between chains.
- A–B · 3161 Ų buried · 54 hydrogen bonds · protein-protein
- G–H · 3154 Ų buried · 55 hydrogen bonds · protein-protein
- C–D · 3145 Ų buried · 54 hydrogen bonds · protein-protein
- E–F · 3136 Ų buried · 60 hydrogen bonds · protein-protein
- B–H · 882 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 4P5M · 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
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 4P5M · PDBe 4P5M · UniProt P20036 · UniProt Q5EP54
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