MolNFT v1 · #136903 · protein + RNA

Crystal structure of LARP1-unique domain DM15 bound 5'TOP RNA sequence

5V7C · La-related protein 1: “Crystal structure of LARP1-unique domain DM15 bound 5'TOP RNA sequence”. X-ray diffraction, 1 pocket (best druggability 0.33). MolNFT v1 #136903 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5V7C
Type: protein + RNA
Length: 152 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: La-related protein 1; RNA (5'-R(*CP*UP*UP*UP*UP*CP*CP*G)-3')
UniProt: Q6PKG0
Pockets: 1 · best druggability 0.33

Structure

x-ray diffraction · 2 distinct chains · 73% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	La-related protein 1	protein	144	73% helix, 0% strand	Q6PKG0
C	RNA (5'-R(CPUPUPUPUPCPCPG)-3')	rna	8	—	—

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	96	0.33	0.73	16	empty

Interfaces

1 interface between chains.

B–C · 630 Å² buried · 16 hydrogen bonds · protein-nucleic

Compared structures

5V7C · Crystal structure of LARP1-unique domain DM15 bound 5'TOP RNA sequence · the same entry in another collection · chain B against B, TM-score 1.00
Q6PKG0 · AlphaFold monomer V2.0 prediction for la-related protein 1 (Q6PKG0) · 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 Q6PKG0
Elsewhere: RCSB PDB 5V7C · PDBe 5V7C · UniProt Q6PKG0

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