Research workbench
The nf-Y transcription factor is structurally and functionally a sequence specific histone
Analyse The nf-Y transcription factor is structurally and functionally a sequence… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AWL
- Type
- protein + DNA
- Length
- 284 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear transcription factor Y subunit alpha; Nuclear transcription factor Y subunit…
- UniProt
- P23511, P25208, Q13952
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 58% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclear transcription factor Y subunit alpha | protein | 62 | 45% helix, 0% strand | P23511 |
| B | Nuclear transcription factor Y subunit beta | protein | 92 | 63% helix, 4% strand | P25208 |
| C | Nuclear transcription factor Y subunit gamma | protein | 80 | 61% helix, 5% strand | Q13952 |
| I | HSP70 promoter fragment | dna | 25 | — | — |
| J | HSP70 promoter fragment | dna | 25 | — | — |
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 535 | 0.71 | 0.80 | 33 | empty |
| 2 | 335 | 0.69 | 0.82 | 33 | empty |
| 3 | 573 | 0.64 | 0.76 | 33 | empty |
| 4 | 206 | 0.61 | 0.83 | 22 | empty |
| 5 | 163 | 0.51 | 0.79 | 24 | empty |
Interfaces
10 interfaces between chains.
- B–C · 2315 Ų buried · 11 hydrogen bonds · protein-protein
- I–J · 1123 Ų buried · 112 hydrogen bonds · nucleic-nucleic
- A–B · 795 Ų buried · 14 hydrogen bonds · protein-protein
- A–I · 538 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–J · 516 Ų buried · 16 hydrogen bonds · protein-nucleic
Compared structures
- 4AWL · The NF-Y transcription factor is structurally and functionally a sequence specific histone · the same entry in another collection · chain J against J, TM-score 1.00
- Q13952 · AlphaFold monomer V2.0 prediction for nuclear transcription factor Y subunit gamma… · a predicted model of the same protein · chain C against A, TM-score 0.96
- P25208 · AlphaFold monomer V2.0 prediction for nuclear transcription factor Y subunit beta (P25208) · a predicted model of the same protein · chain B against A, TM-score 0.94
- P23511 · AlphaFold monomer V2.0 prediction for nuclear transcription factor Y subunit alpha… · a predicted model of the same protein · chain A against A, TM-score 0.82
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 P23511
- Every structure of UniProt P25208
- Every structure of UniProt Q13952
- Elsewhere: RCSB PDB 4AWL · PDBe 4AWL · UniProt P23511 · UniProt P25208 · UniProt Q13952
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