MolNFT v1 · #112450 · protein + RNA

Structure of the brat-nhl domain bound to consensus RNA motif

4ZLR · Brain tumor protein: “Structure of the brat-nhl domain bound to consensus RNA motif”. X-ray diffraction, 1 ligand (SO4), 3 pockets (best druggability 0.75). MolNFT v1 #112450 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 4ZLR
Type: protein + RNA
Length: 570 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Brain tumor protein; RNA (5'-R(*UP*UP*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3')
UniProt: Q8MQJ9
Ligands: SO4
Pockets: 3 · best druggability 0.75

Structure

x-ray diffraction · 3 distinct chains · 1% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Brain tumor protein	protein	278	1% helix, 51% strand	Q8MQJ9
C	RNA (5'-R(UPUPGPUPUPGPUPUPUPUPUPUPUPU)-3')	rna	14	—	—
B	Brain tumor protein	protein	278	1% helix, 51% strand	Q8MQJ9

Ligands and binding sites

SO4 · Sulfate ion · ion · 9 copies · chains A, B
PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · chains A
PG4 · Tetraethylene glycol · additive · chains B
1PE · Pentaethylene glycol · additive · chains B

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

Pockets

3 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	718	0.75	0.81	81	empty
2	414	0.73	0.83	49	SO4
3	454	0.71	0.82	43	SO4

Interfaces

3 interfaces between chains.

C–B · 899 Å² buried · 27 hydrogen bonds · protein-nucleic
A–C · 850 Å² buried · 33 hydrogen bonds · protein-nucleic
A–B · 625 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

4ZLR · Structure of the Brat-NHL domain bound to consensus RNA motif · the same entry in another collection · chain A against A, TM-score 1.00
Q8MQJ9 · AlphaFold monomer V2.0 prediction for brain tumor protein (Q8MQJ9) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 Q8MQJ9
Elsewhere: RCSB PDB 4ZLR · PDBe 4ZLR · UniProt Q8MQJ9

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