MolNFT v1 · #175748 · protein + RNA

Cryo-EM structure of a pre-catalytic group II intron rnp

7D0F · RNA (738-mer): “Cryo-EM structure of a pre-catalytic group II intron rnp”. Electron microscopy, 20 pockets (best druggability 0.87). MolNFT v1 #175748 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7D0F
Type: protein + RNA
Length: 1,185 residues
Chains: 2
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (738-mer); Group II intron-encoded protein ltra
EC: 2.7.7.49, 3.1.-.-
UniProt: P0A3U0
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 2 distinct chains · 36% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA (738-mer)	rna	738	—	—
C	Group II intron-encoded protein ltra (EC 2.7.7.49, 3.1.-.-)	protein	447	36% helix, 4% strand	P0A3U0

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1102	0.87	0.88	129	empty
2	912	0.80	0.83	102	empty
3	487	0.74	0.84	40	empty
4	320	0.73	0.86	40	empty
5	1069	0.73	0.78	50	empty

Interfaces

1 interface between chains.

A–C · 3089 Å² buried · 98 hydrogen bonds · protein-nucleic

Compared structures

7D0F · cryo-EM structure of a pre-catalytic group II intron RNP · the same entry in another collection · chain A against A, TM-score 1.00
P0A3U0 · AlphaFold monomer V2.0 prediction for group II intron-encoded protein ltra (P0A3U0) · 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 P0A3U0
Elsewhere: RCSB PDB 7D0F · PDBe 7D0F · UniProt P0A3U0

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