Research workbench
Oxime side-chain cross-links in the GCN4-P1 dimeric coiled coil: cyclic product
Analyse Oxime side-chain cross-links in the GCN4-P1 dimeric coiled coil: cyclic product in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HU6
- Type
- protein
- Length
- 127 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- General control protein GCN4
- UniProt
- P03069
- Ligands
- ACE
- Pockets
- 2 · best druggability 0.36
Structure
x-ray diffraction · 2 distinct chains · 90% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | General control protein GCN4 | protein | 32 | 91% helix, 0% strand | P03069 |
| B | General control protein GCN4 | protein | 31 | 90% helix, 0% strand | P03069 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 3 copies · chains B, C, D
- ACT · Acetate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 94 | 0.36 | 0.75 | 16 | ACT |
| 2 | 97 | 0.35 | 0.74 | 12 | empty |
Interfaces
6 interfaces between chains.
- A–B · 970 Ų buried · 2 hydrogen bonds · protein-protein
- C–D · 935 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 456 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 175 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 162 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified, 4 covalent (nonstandard, covalent ligand).
Compared structures
- 4HU6 · Oxime side-chain cross-links in the GCN4-p1 dimeric coiled coil: Cyclic product · the same entry in another collection · chain D against D, TM-score 1.00
- P03069 · AlphaFold monomer V2.0 prediction for general control transcription factor GCN4 (P03069) · a predicted model of the same protein · chain B against A, TM-score 0.91
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 P03069
- Elsewhere: RCSB PDB 4HU6 · PDBe 4HU6 · UniProt P03069
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