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A novel DNA recognition mode by nf-kb P65 homodimer

Analyse A novel DNA recognition mode by nf-kb P65 homodimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2RAM
Type: protein + DNA
Length: 586 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'- D(*CP*GP*GP*CP*TP*GP*GP*AP*AP*AP*TP*(5IU)P*(5IU) P*CP*CP*AP*GP*CP*CP*G)-3')…
UniProt: Q04207
Ligands: DTV
Pockets: 6 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C, D	DNA (5'- D(CPGPGPCPTPGPGPAPAPAPTP(5IU)P(5IU) PCPCPAPGPCPCPG)-3')	dna	20	—	—
A, B	Protein (transcription factor nf-kb P65)	protein	273	6% helix, 39% strand	Q04207

Ligands and binding sites

DTV · (2S,3S)-1,4-dimercaptobutane-2,3-diol · ligand · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1138	0.81	0.83	96	empty
2	495	0.62	0.76	50	empty
3	65	0.50	0.85	17	empty
4	198	0.47	0.75	27	empty
5	67	0.38	0.79	18	empty

Interfaces

6 interfaces between chains.

C–D · 881 Å² buried · 103 hydrogen bonds · nucleic-nucleic
A–B · 689 Å² buried · 8 hydrogen bonds · protein-protein
C–A · 615 Å² buried · 9 hydrogen bonds · protein-nucleic
D–B · 577 Å² buried · 9 hydrogen bonds · protein-nucleic
D–A · 261 Å² buried · 9 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 4 modified (nucleotide modification).

Compared structures

2RAM · A novel DNA recognition mode by nf-kb P65 homodimer · the same entry in another collection · chain C against C, TM-score 1.00
Q04207 · AlphaFold monomer V2.0 prediction for transcription factor P65 (Q04207) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q04207
Elsewhere: RCSB PDB 2RAM · PDBe 2RAM · UniProt Q04207

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