Research workbench
Crystal structure of DNA-bound CCT/NF-YB/YC complex (HD1CCT/GHD8/OSNF- YC2)
Analyse Crystal structure of DNA-bound CCT/NF-YB/YC complex (HD1CCT/GHD8/OSNF- YC2) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7C9O
- Type
- protein + DNA
- Length
- 260 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Zinc finger protein HD1; Nuclear transcription factor Y subunit B-11; Nuclear…
- UniProt
- Q9FDX8, Q0J7P4, A6BLW4
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 64% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Zinc finger protein HD1 | protein | 45 | 51% helix, 9% strand | Q9FDX8 |
| B | Nuclear transcription factor Y subunit B-11 | protein | 85 | 69% helix, 5% strand | Q0J7P4 |
| C | Nuclear transcription factor Y subunit C-2 | protein | 80 | 65% helix, 5% strand | A6BLW4 |
| D | DNA (25-mer) | dna | 25 | — | — |
| E | DNA (25-mer) | dna | 25 | — | — |
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 578 | 0.71 | 0.79 | 37 | empty |
| 2 | 589 | 0.66 | 0.77 | 46 | empty |
| 3 | 54 | 0.60 | 0.92 | 20 | empty |
| 4 | 156 | 0.48 | 0.78 | 17 | empty |
Interfaces
10 interfaces between chains.
- B–C · 2428 Ų buried · 22 hydrogen bonds · protein-protein
- D–E · 1084 Ų buried · 108 hydrogen bonds · nucleic-nucleic
- A–C · 700 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 571 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–B · 538 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 7C9O · Crystal structure of DNA-bound CCT/NF-YB/YC complex (HD1CCT/GHD8/OsNF-YC2) · the same entry in another collection · chain B against B, TM-score 1.00
- Q0J7P4 · AlphaFold monomer V2.0 prediction for nuclear transcription factor Y subunit B-11 (Q0J7P4) · a predicted model of the same protein · chain B against A, TM-score 0.94
- A6BLW4 · AlphaFold monomer V2.0 prediction for nuclear transcription factor Y subunit C-2 (A6BLW4) · a predicted model of the same protein · chain C against A, TM-score 0.94
- Q9FDX8 · AlphaFold monomer V2.0 prediction for zinc finger protein HD1 (Q9FDX8) · a predicted model of the same protein · chain A against A, TM-score 0.46
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 Q9FDX8
- Every structure of UniProt Q0J7P4
- Every structure of UniProt A6BLW4
- Elsewhere: RCSB PDB 7C9O · PDBe 7C9O · UniProt Q9FDX8 · UniProt Q0J7P4 · UniProt A6BLW4
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