Research workbench
Crystal structure of mouse apolipoprotein a-I binding protein
Analyse Crystal structure of mouse apolipoprotein a-I binding protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DG2
- Type
- protein
- Length
- 1,398 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Apolipoprotein a-I binding protein
- Ligands
- SO4, CL
- Pockets
- 14 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Apolipoprotein a-I binding protein | protein | 233 | 38% helix, 16% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 6 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 831 | 0.84 | 0.87 | 107 | empty |
| 2 | 800 | 0.74 | 0.79 | 94 | empty |
| 3 | 92 | 0.73 | 0.95 | 28 | empty |
| 4 | 89 | 0.72 | 0.95 | 27 | empty |
| 5 | 161 | 0.67 | 0.87 | 24 | SO4 |
Interfaces
9 interfaces between chains.
- C–D · 1450 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 1435 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 805 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 385 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 380 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 modified (engineered).
Compared structures
- 2DG2 · Crystal Structure of Mouse Apolipoprotein A-I Binding Protein · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 2DG2 · PDBe 2DG2
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