MolNFT v1 · #72539 · protein + DNA

Crystal structure of a dimer of notch transcription complex trimers on HES1 DNA

3NBN · Recombining binding protein suppressor of hairless: “Crystal structure of a dimer of notch transcription complex trimers on HES1 DNA”. X-ray diffraction, 20 pockets (best druggability 0.81). MolNFT v1 #72539 on GenesisL1: 3D…

PDB: 3NBN
Type: protein + DNA
Length: 1,422 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Recombining binding protein suppressor of hairless; Neurogenic locus notch homolog…
UniProt: Q06330, P46531, Q92585
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 5 distinct chains · 23% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Recombining binding protein suppressor of hairless	protein	423	3% helix, 37% strand	Q06330
B, E	Neurogenic locus notch homolog protein 1	protein	196	48% helix, 2% strand	P46531
C, F	Mastermind-like protein 1	protein	55	80% helix, 0% strand	Q92585
X	DNA, HES1 promoter	dna	37	—	—
Y	DNA, HES1 promoter	dna	37	—	—

Pockets

20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1076	0.81	0.83	95	empty
2	1144	0.80	0.82	105	empty
3	534	0.76	0.84	58	empty
4	588	0.75	0.82	53	empty
5	171	0.71	0.89	16	empty

Interfaces

12 interfaces between chains.

X–Y · 1636 Å² buried · 128 hydrogen bonds · nucleic-nucleic
D–F · 1301 Å² buried · 15 hydrogen bonds · protein-protein
A–C · 1298 Å² buried · 18 hydrogen bonds · protein-protein
D–E · 1155 Å² buried · 12 hydrogen bonds · protein-protein
A–B · 1129 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

3NBN · Crystal structure of a dimer of Notch Transcription Complex trimers on HES1 DNA · the same entry in another collection · chain Y against Y, TM-score 1.00
P46531 · AlphaFold monomer V2.0 prediction for neurogenic locus notch homolog protein 1 (P46531) · a predicted model of the same protein · chain B against A, TM-score 0.98
Q06330 · AlphaFold monomer V2.0 prediction for recombining binding protein suppressor of hairless… · a predicted model of the same protein · chain A against A, TM-score 0.97
Q92585 · AlphaFold monomer V2.0 prediction for mastermind-like protein 1 (Q92585) · a predicted model of the same protein · chain C against A, TM-score 0.75

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 Q06330
Every structure of UniProt P46531
Every structure of UniProt Q92585
Elsewhere: RCSB PDB 3NBN · PDBe 3NBN · UniProt Q06330 · UniProt P46531 · UniProt Q92585

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