Research workbench
Ccaat-binding complex from aspergillus fumigatus with cyca DNA
Analyse Ccaat-binding complex from aspergillus fumigatus with cyca DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Y35
- Type
- protein + DNA
- Length
- 302 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ccaat-binding transcription factor subunit hapb; Ccaat-binding factor complex subunit…
- UniProt
- Q4X049, Q4WDM9
- Ligands
- SO3
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 63% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ccaat-binding transcription factor subunit hapb | protein | 53 | 49% helix, 4% strand | Q4X049 |
| B | Ccaat-binding factor complex subunit hapc | protein | 92 | 74% helix, 4% strand | — |
| C | Ccaat-binding factor complex subunit hape | protein | 107 | 62% helix, 4% strand | Q4WDM9 |
| D | DNA (25-mer) | dna | 25 | — | — |
| E | DNA (25-mer) | dna | 25 | — | — |
Ligands and binding sites
- SO3 · Sulfite ion · ion · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 690 | 0.78 | 0.83 | 57 | empty |
| 2 | 470 | 0.67 | 0.79 | 31 | empty |
| 3 | 178 | 0.55 | 0.80 | 29 | empty |
| 4 | 174 | 0.48 | 0.76 | 24 | empty |
| 5 | 105 | 0.35 | 0.74 | 19 | empty |
Interfaces
10 interfaces between chains.
- B–C · 2830 Ų buried · 23 hydrogen bonds · protein-protein
- D–E · 1080 Ų buried · 103 hydrogen bonds · nucleic-nucleic
- A–B · 763 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 544 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–D · 512 Ų buried · 13 hydrogen bonds · protein-nucleic
Compared structures
- 6Y35 · CCAAT-binding complex from Aspergillus fumigatus with cycA DNA · 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
- Every structure of UniProt Q4X049
- Every structure of UniProt Q4WDM9
- Elsewhere: RCSB PDB 6Y35 · PDBe 6Y35 · UniProt Q4X049 · UniProt Q4WDM9
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