Research workbench

Arabidopsis nf-Y/CCAAT-box complex

Analyse Arabidopsis nf-Y/CCAAT-box complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6R2V
Type: protein + DNA
Length: 300 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nuclear transcription factor Y subunit a-6; Nf-YB2; Nf-YC3; Ft (-5KB) ccaat-box 5'; Ft…
UniProt: Q9LVJ7, A0A178UPH7, A0A178WGU5
Pockets: 7 · best druggability 0.70

Structure

x-ray diffraction · 5 distinct chains · 55% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nuclear transcription factor Y subunit a-6	protein	62	37% helix, 3% strand	Q9LVJ7
B	Nf-YB2	protein	93	73% helix, 4% strand	A0A178UPH7
C	Nf-YC3	protein	95	49% helix, 4% strand	A0A178WGU5
I	Ft (-5KB) ccaat-box 5'	dna	25	—	—
J	Ft (-5KB) ccaat-box 3'	dna	25	—	—

Pockets

7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	599	0.70	0.79	36	empty
2	184	0.63	0.84	20	empty
3	219	0.63	0.83	24	empty
4	536	0.61	0.75	35	empty
5	162	0.53	0.80	22	empty

Interfaces

10 interfaces between chains.

B–C · 2509 Å² buried · 18 hydrogen bonds · protein-protein
I–J · 1047 Å² buried · 98 hydrogen bonds · nucleic-nucleic
A–B · 851 Å² buried · 11 hydrogen bonds · protein-protein
A–I · 570 Å² buried · 13 hydrogen bonds · protein-nucleic
A–J · 527 Å² buried · 14 hydrogen bonds · protein-nucleic

Compared structures

6R2V · Arabidopsis NF-Y/CCAAT-box complex · the same entry in another collection · chain A against A, TM-score 1.00
Q9LVJ7 · AlphaFold monomer V2.0 prediction for nuclear transcription factor Y subunit a-6 (Q9LVJ7) · a predicted model of the same protein · chain A against A, TM-score 0.80

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 Q9LVJ7
Every structure of UniProt A0A178UPH7
Every structure of UniProt A0A178WGU5
Elsewhere: RCSB PDB 6R2V · PDBe 6R2V · UniProt Q9LVJ7 · UniProt A0A178UPH7 · UniProt A0A178WGU5

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