Research workbench
Ccaat-binding complex from aspergillus nidulans with DNA
Analyse Ccaat-binding complex from aspergillus nidulans with DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4G92
- Type
- protein + DNA
- Length
- 320 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hapb protein; Transcription factor hapc (eurofung); Hape; DNA
- UniProt
- P87249, Q5B5Z6, Q5AYY8
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 61% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hapb protein | protein | 61 | 43% helix, 3% strand | P87249 |
| B | Transcription factor hapc (eurofung) | protein | 92 | 73% helix, 4% strand | Q5B5Z6 |
| C | Hape | protein | 117 | 61% helix, 3% strand | Q5AYY8 |
| D | DNA | dna | 25 | — | — |
| E | DNA | dna | 25 | — | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains B, E, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 997 | 0.78 | 0.80 | 82 | empty |
| 2 | 697 | 0.68 | 0.76 | 41 | SO4 |
| 3 | 150 | 0.57 | 0.83 | 26 | empty |
| 4 | 115 | 0.41 | 0.76 | 11 | SO4 |
| 5 | 108 | 0.39 | 0.75 | 17 | empty |
Interfaces
10 interfaces between chains.
- B–C · 2977 Ų buried · 28 hydrogen bonds · protein-protein
- D–E · 1055 Ų buried · 91 hydrogen bonds · nucleic-nucleic
- A–B · 872 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 572 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–D · 521 Ų buried · 16 hydrogen bonds · protein-nucleic
Compared structures
- 4G92 · CCAAT-binding complex from Aspergillus nidulans with 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 P87249
- Every structure of UniProt Q5B5Z6
- Every structure of UniProt Q5AYY8
- Elsewhere: RCSB PDB 4G92 · PDBe 4G92 · UniProt P87249 · UniProt Q5B5Z6 · UniProt Q5AYY8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.