MolNFT v1 · #8696 · protein + DNA

Crystal structure of ternary protein-DNA COMPLEX3

1H8A · CAAT/ENHANCER binding protein beta: “Crystal structure of ternary protein-DNA COMPLEX3”. X-ray diffraction, 7 pockets (best druggability 0.67). MolNFT v1 #8696 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1H8A
Type: protein + DNA
Length: 292 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: CAAT/ENHANCER binding protein beta; Myb transforming protein…
UniProt: P17676, P01104
Pockets: 7 · best druggability 0.67

Structure

x-ray diffraction · 5 distinct chains · 76% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	CAAT/ENHANCER binding protein beta	protein	68	88% helix, 0% strand	P17676
B	CAAT/ENHANCER binding protein beta	protein	67	91% helix, 0% strand	P17676
C	Myb transforming protein	protein	105	59% helix, 0% strand	P01104
D	DNA(5'-(GPAPTPGPTPGPGPCPGPCPAP APTPCPCPTPTPAPAPCPGPGPAPCPTPG)-3')	dna	26	—	—
E	DNA(5'-(CPCPAPGPTPCPCPGPTPTPAP APGPGPAPTPTPGPCPGPCPCPAPCPAPT)-3')	dna	26	—	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	572	0.67	0.77	37	empty
2	113	0.52	0.82	19	empty
3	140	0.52	0.81	25	empty
4	170	0.48	0.77	16	empty
5	194	0.47	0.75	23	empty

Interfaces

8 interfaces between chains.

D–E · 1121 Å² buried · 85 hydrogen bonds · nucleic-nucleic
A–B · 1049 Å² buried · 6 hydrogen bonds · protein-protein
C–D · 609 Å² buried · 12 hydrogen bonds · protein-nucleic
C–E · 540 Å² buried · 9 hydrogen bonds · protein-nucleic
A–D · 383 Å² buried · 12 hydrogen bonds · protein-nucleic

Compared structures

1H8A · Crystal structure of ternary protein-DNA COMPLEX3 · the same entry in another collection · chain B against B, TM-score 1.00
P17676 · AlphaFold monomer V2.0 prediction for CCAAT/ENHANCER-binding protein beta (P17676) · a predicted model of the same protein · chain A against A, TM-score 0.89

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 P17676
Every structure of UniProt P01104
Elsewhere: RCSB PDB 1H8A · PDBe 1H8A · UniProt P17676 · UniProt P01104

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