Research workbench
Ccaat-binding complex from aspergillus nidulans with ccca DNA
Analyse Ccaat-binding complex from aspergillus nidulans with ccca DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Y37
- Type
- protein + DNA
- Length
- 319 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hapb; Transcription factor hapc (eurofung); CBFD_NFYB_HMF domain-containing protein; DNA…
- UniProt
- G5EAZ0, Q5B5Z6, Q5AYY8
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 60% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hapb | protein | 60 | 45% helix, 3% strand | G5EAZ0 |
| B | Transcription factor hapc (eurofung) | protein | 91 | 70% helix, 4% strand | Q5B5Z6 |
| C | CBFD_NFYB_HMF domain-containing protein | protein | 118 | 60% helix, 3% strand | Q5AYY8 |
| D | DNA (25-mer) | dna | 25 | — | — |
| E | DNA (25-mer) | dna | 25 | — | — |
Ligands and binding sites
- GOL · Glycerol · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 611 | 0.74 | 0.81 | 41 | empty |
| 2 | 598 | 0.69 | 0.78 | 45 | empty |
| 3 | 222 | 0.62 | 0.82 | 30 | empty |
| 4 | 140 | 0.45 | 0.76 | 20 | empty |
| 5 | 110 | 0.41 | 0.77 | 12 | empty |
Interfaces
10 interfaces between chains.
- B–C · 2983 Ų buried · 35 hydrogen bonds · protein-protein
- D–E · 1080 Ų buried · 98 hydrogen bonds · nucleic-nucleic
- A–B · 850 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 528 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–D · 520 Ų buried · 13 hydrogen bonds · protein-nucleic
Compared structures
- 6Y37 · CCAAT-binding complex from Aspergillus nidulans with cccA 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 G5EAZ0
- Every structure of UniProt Q5B5Z6
- Every structure of UniProt Q5AYY8
- Elsewhere: RCSB PDB 6Y37 · PDBe 6Y37 · UniProt G5EAZ0 · UniProt Q5B5Z6 · UniProt Q5AYY8
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