Research workbench
Crystal structure of the N-terminal kh domain of human BICC1
Analyse Crystal structure of the N-terminal kh domain of human BICC1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GY4
- Type
- protein
- Length
- 293 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein bicaudal C homolog 1
- UniProt
- Q9H694
- Ligands
- SO4, CL
- Pockets
- 2 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein bicaudal C homolog 1 | protein | 68 | 53% helix, 25% strand | Q9H694 |
| B | Protein bicaudal C homolog 1 | protein | 80 | 50% helix, 21% strand | Q9H694 |
| C | Protein bicaudal C homolog 1 | protein | 75 | 53% helix, 23% strand | Q9H694 |
| D | Protein bicaudal C homolog 1 | protein | 70 | 50% helix, 24% strand | Q9H694 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains B, C
- CL · Chloride ion · ion · chains C
- XPE · 3,6,9,12,15,18,21,24,27-nonaoxanonacosane-1,29-diol · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 634 | 0.65 | 0.75 | 56 | empty |
| 2 | 62 | 0.33 | 0.76 | 14 | empty |
Interfaces
4 interfaces between chains.
- A–D · 394 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 367 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 156 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 113 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6GY4 · Crystal structure of the N-terminal KH domain of human BICC1 · the same entry in another collection · chain D against D, TM-score 1.00
- Q9H694 · AlphaFold monomer V2.0 prediction for protein bicaudal C homolog 1 (Q9H694) · a predicted model of the same protein · chain A against A, TM-score 0.87
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 Q9H694
- Elsewhere: RCSB PDB 6GY4 · PDBe 6GY4 · UniProt Q9H694
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