MolNFT v1 · #172888 · protein
Nf-Y bound to suramin inhibitor
7AH8 · Nuclear transcription factor Y subunit beta: “Nf-Y bound to suramin inhibitor”. X-ray diffraction, 1 ligand (SVR), 1 pocket (best druggability 0.69). MolNFT v1 #172888 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7AH8
- Type
- protein
- Length
- 336 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear transcription factor Y subunit beta; Isoform 6 of nuclear transcription factor Y…
- UniProt
- P25208, Q13952
- Ligands
- SVR
- Pockets
- 1 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 66% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclear transcription factor Y subunit beta | protein | 88 | 69% helix, 3% strand | P25208 |
| B | Isoform 6 of nuclear transcription factor Y subunit gamma | protein | 79 | 63% helix, 4% strand | Q13952 |
| C | Nuclear transcription factor Y subunit beta | protein | 89 | 69% helix, 3% strand | P25208 |
| D | Isoform 6 of nuclear transcription factor Y subunit gamma | protein | 80 | 64% helix, 4% strand | Q13952 |
Ligands and binding sites
- SVR · 8,8'-[carbonylbis[imino-3,1-phenylenecarbonylimino(4-methyl-3,1-phenylene)carbonylimino]]bis-1,3,5-naphthalenetrisulfonic acid · ligand · chains A, B, C, D
- GOL · Glycerol · additive · chains B, D
- FLC · Citrate anion · additive
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 536 | 0.69 | 0.78 | 42 | GOL, SVR |
Interfaces
5 interfaces between chains.
- C–D · 2391 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 2344 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 111 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 63 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 54 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7AH8 · NF-Y bound to suramin inhibitor · the same entry in another collection · chain D against D, 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 B against A, TM-score 0.97
- P25208 · AlphaFold monomer V2.0 prediction for nuclear transcription factor Y subunit beta (P25208) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P25208
- Every structure of UniProt Q13952
- Elsewhere: RCSB PDB 7AH8 · PDBe 7AH8 · UniProt P25208 · UniProt Q13952
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