Research workbench
Crystal structure of arabidopsis co cct domain in complex with nf- YB3/YC4 and ft CORE2 DNA
Analyse Crystal structure of arabidopsis co cct domain in complex with nf- YB3/YC4 and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CVO
- Type
- protein + DNA
- Length
- 454 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chimera of nuclear transcription factor Y subunit C-4 and zinc finger protein constans…
- UniProt
- Q9FMV5, Q39057, O23310
- Pockets
- 8 · best druggability 0.69
Structure
x-ray diffraction · 5 distinct chains · 66% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chimera of nuclear transcription factor Y subunit C-4 and zinc finger protein constans | protein | 130 | 58% helix, 6% strand | Q9FMV5, Q39057 |
| B, G | Nuclear transcription factor Y subunit B-3 | protein | 88 | 72% helix, 5% strand | O23310 |
| D | Ft CORE2 DNA forward strand | dna | 25 | — | — |
| E | Ft CORE2 DNA reverse strand | dna | 25 | — | — |
| F | Chimera of nuclear transcription factor Y subunit C-4 and zinc finger protein constans | protein | 98 | 69% helix, 4% strand | Q9FMV5, Q39057 |
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 542 | 0.69 | 0.79 | 33 | empty |
| 2 | 222 | 0.62 | 0.82 | 31 | empty |
| 3 | 74 | 0.62 | 0.91 | 21 | empty |
| 4 | 215 | 0.56 | 0.80 | 31 | empty |
| 5 | 192 | 0.55 | 0.79 | 23 | empty |
Interfaces
9 interfaces between chains.
- A–B · 2927 Ų buried · 27 hydrogen bonds · protein-protein
- F–G · 2696 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 1071 Ų buried · 100 hydrogen bonds · nucleic-nucleic
- A–E · 769 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–D · 750 Ų buried · 18 hydrogen bonds · protein-nucleic
Compared structures
- 7CVO · crystal structure of Arabidopsis CO CCT domain in complex with NF-YB3/YC4 and FT CORE2 DNA · the same entry in another collection · chain G against G, TM-score 1.00
- O23310 · AlphaFold monomer V2.0 prediction for nuclear transcription factor Y subunit B-3 (O23310) · a predicted model of the same protein · chain B against A, TM-score 0.95
- Q9FMV5 · AlphaFold monomer V2.0 prediction for nuclear transcription factor Y subunit C-4 (Q9FMV5) · a predicted model of the same protein · chain F against A, TM-score 0.77
- Q39057 · AlphaFold monomer V2.0 prediction for zinc finger protein constans (Q39057) · a predicted model of the same protein · chain F against A, TM-score 0.26
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 Q9FMV5
- Every structure of UniProt Q39057
- Every structure of UniProt O23310
- Elsewhere: RCSB PDB 7CVO · PDBe 7CVO · UniProt Q9FMV5 · UniProt Q39057 · UniProt O23310
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