MolNFT v1 · #16365 · protein + DNA

Crystal structure of C/EBPALPHA-DNA complex

1NWQ · 5'- D(*TP*TP*CP*CP*TP*AP*TP*TP*GP*CP*GP*CP*AP*AP*TP*CP*CP*AP…: “Crystal structure of C/EBPALPHA-DNA complex”. X-ray diffraction, 3 pockets (best druggability 0.66). MolNFT v1 #16365 on GenesisL1: 3D structure, binding sites and…

PDB: 1NWQ
Type: protein + DNA
Length: 162 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'- D(*TP*TP*CP*CP*TP*AP*TP*TP*GP*CP*GP*CP*AP*AP*TP*CP*CP*AP*GP *TP*T)-3'; 5'…
UniProt: P05554
Pockets: 3 · best druggability 0.66

Structure

x-ray diffraction · 3 distinct chains · 95% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	5'- D(TPTPCPCPTPAPTPTPGPCPGPCPAPAPTPCPCPAPGP TP*T)-3'	dna	21	—	—
D	5'- D(APAPAPCPTPGPGPAPTPTPGPCPGPCPAPAPTPAPGP GP*A)-3'	dna	21	—	—
A, C	CCAAT/ENHANCER binding protein alpha	protein	60	95% helix, 0% strand	P05554

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	530	0.66	0.78	30	empty
2	175	0.48	0.77	16	empty
3	180	0.47	0.76	15	empty

Interfaces

6 interfaces between chains.

A–C · 889 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 867 Å² buried · 84 hydrogen bonds · nucleic-nucleic
B–C · 376 Å² buried · 13 hydrogen bonds · protein-nucleic
B–A · 369 Å² buried · 6 hydrogen bonds · protein-nucleic
D–C · 329 Å² buried · 6 hydrogen bonds · protein-nucleic

Compared structures

1NWQ · Crystal structure of C/EBPALPHA-DNA complex · the same entry in another collection · chain B against B, TM-score 1.00
P05554 · AlphaFold monomer V2.0 prediction for CCAAT/ENHANCER-binding protein alpha (P05554) · 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 P05554
Elsewhere: RCSB PDB 1NWQ · PDBe 1NWQ · UniProt P05554

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