MolNFT v1 · #161710 · protein
Nf-YB/C heterodimer in complex with nf-ya-derived peptide stabilized with C11-hydrocarbon linker
6QMS · Nuclear transcription factor Y subunit alpha: “Nf-YB/C heterodimer in complex with nf-ya-derived peptide stabilized with C11-hydrocarbon linker”. X-ray diffraction, 1 ligand (ACE), 1 pocket (best druggability 0.30). MolNFT v1…
- PDB
- 6QMS
- Type
- protein
- Length
- 184 residues
- Chains
- 3
- 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
- Ligands
- ACE
- Pockets
- 1 · best druggability 0.30
Structure
x-ray diffraction · 3 distinct chains · 66% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclear transcription factor Y subunit alpha | protein | 17 | 59% helix, 0% strand | P23511 |
| B | Nuclear transcription factor Y subunit beta | protein | 87 | 71% helix, 5% strand | P25208 |
| C | Nuclear transcription factor Y subunit gamma | protein | 80 | 63% helix, 5% strand | Q13952 |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.30 | 0.76 | 13 | empty |
Interfaces
3 interfaces between chains.
- B–C · 2398 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 436 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 288 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified, 1 covalent (nonstandard, covalent ligand).
Compared structures
- 6QMS · NF-YB/C Heterodimer in Complex with NF-YA-derived Peptide Stabilized with C11-Hydrocarbon… · the same entry in another collection · chain A against A, 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 0.95
- 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 0.93
- 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 0.62
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 6QMS · PDBe 6QMS · UniProt P23511 · UniProt P25208 · UniProt Q13952
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