MolNFT v1 · #153960 · protein + DNA

Crystal structure of RBM38 in complex with single-stranded DNA

6JVY · RNA-binding protein 38: “Crystal structure of RBM38 in complex with single-stranded DNA”. X-ray diffraction, 1 ligand (SO4). MolNFT v1 #153960 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6JVY
Type: protein + DNA
Length: 93 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA-binding protein 38; DNA (5'-D(*TP*GP*TP*GP*TP*GP*TP*GP*TP*GP*TP*G)-3')
UniProt: Q9H0Z9
Ligands: SO4

Structure

x-ray diffraction · 2 distinct chains · 27% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA-binding protein 38	protein	86	27% helix, 35% strand	Q9H0Z9
B	DNA (5'-D(TPGPTPGPTPGPTPGPTPGPTPG)-3')	dna	7	—	—

Ligands and binding sites

SO4 · Sulfate ion · ion · chains A

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

Interfaces

1 interface between chains.

A–B · 642 Å² buried · 16 hydrogen bonds · protein-nucleic

Compared structures

6JVY · Crystal structure of RBM38 in complex with single-stranded DNA · the same entry in another collection · chain A against A, TM-score 1.00
Q9H0Z9 · AlphaFold monomer V2.0 prediction for RNA-binding protein 38 (Q9H0Z9) · 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 Q9H0Z9
Elsewhere: RCSB PDB 6JVY · PDBe 6JVY · UniProt Q9H0Z9

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