Research workbench
Crystal structure of mouse apolipoprotein a-I binding protein in complex with thymidine
Analyse Crystal structure of mouse apolipoprotein a-I binding protein in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ROE
- 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
- UniProt
- Q8K4Z3
- Ligands
- THM
- Pockets
- 17 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Apolipoprotein a-I-binding protein | protein | 233 | 38% helix, 15% strand | Q8K4Z3 |
Ligands and binding sites
- THM · Thymidine · ligand · 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
17 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 741 | 0.76 | 0.81 | 87 | empty |
| 2 | 81 | 0.73 | 0.96 | 24 | empty |
| 3 | 692 | 0.71 | 0.78 | 80 | empty |
| 4 | 195 | 0.71 | 0.88 | 28 | THM |
| 5 | 208 | 0.70 | 0.87 | 32 | THM |
Interfaces
10 interfaces between chains.
- A–C · 1433 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 1389 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 1358 Ų buried · 16 hydrogen bonds · protein-protein
- C–E · 735 Ų buried · 3 hydrogen bonds · protein-protein
- D–F · 567 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 modified (engineered).
Compared structures
- 3ROE · Crystal Structure of Mouse Apolipoprotein A-I Binding Protein in Complex with Thymidine · the same entry in another collection · chain C against C, TM-score 1.00
- Q8K4Z3 · AlphaFold monomer V2.0 prediction for NAD(P)H-hydrate epimerase (Q8K4Z3) · a predicted model of the same protein · 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
- Every structure of UniProt Q8K4Z3
- Elsewhere: RCSB PDB 3ROE · PDBe 3ROE · UniProt Q8K4Z3
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