Research workbench
Hape-P88L mutant ccaat-binding complex from aspergillus nidulans with cyca DNA
Analyse Hape-P88L mutant ccaat-binding complex from aspergillus nidulans 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
- 6Y39
- Type
- protein + DNA
- Length
- 755 residues
- Chains
- 11
- 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
- Ligands
- CL
- Pockets
- 15 · best druggability 0.64
Structure
x-ray diffraction · 9 distinct chains · 66% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hapb | protein | 28 | 50% helix, 0% strand | G5EAZ0 |
| B | Transcription factor hapc (eurofung) | protein | 90 | 71% helix, 4% strand | Q5B5Z6 |
| C, I | CBFD_NFYB_HMF domain-containing protein | protein | 118 | 64% helix, 3% strand | Q5AYY8 |
| D | Hapb | protein | 29 | 62% helix, 0% strand | G5EAZ0 |
| E, H | Transcription factor hapc (eurofung) | protein | 87 | 71% helix, 5% strand | Q5B5Z6 |
| F | CBFD_NFYB_HMF domain-containing protein | protein | 117 | 64% helix, 3% strand | Q5AYY8 |
| G | Hapb | protein | 31 | 65% helix, 0% strand | G5EAZ0 |
| J | DNA (25 mer) | dna | 25 | — | — |
| K | DNA (25 mer) | dna | 25 | — | — |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains E, F, H, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 545 | 0.64 | 0.77 | 41 | empty |
| 2 | 419 | 0.64 | 0.78 | 28 | empty |
| 3 | 436 | 0.62 | 0.77 | 28 | empty |
| 4 | 429 | 0.59 | 0.75 | 30 | empty |
| 5 | 229 | 0.48 | 0.74 | 30 | empty |
Interfaces
23 interfaces between chains.
- H–I · 2867 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 2843 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 2825 Ų buried · 23 hydrogen bonds · protein-protein
- J–K · 1027 Ų buried · 109 hydrogen bonds · nucleic-nucleic
- D–E · 569 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6Y39 · HapE-P88L mutant CCAAT-binding complex from Aspergillus nidulans 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 G5EAZ0
- Every structure of UniProt Q5B5Z6
- Every structure of UniProt Q5AYY8
- Elsewhere: RCSB PDB 6Y39 · PDBe 6Y39 · UniProt G5EAZ0 · UniProt Q5B5Z6 · UniProt Q5AYY8
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