MolNFT v2 · #220518 · protein + RNA

Structure of a group II intron ribonucleoprotein in the pre-branching (pre-1F) state

8T2S · Group II intron reverse transcriptase/maturase: “Structure of a group II intron ribonucleoprotein in the pre-branching (pre-1F) state”. Electron microscopy at 3.0, 2 ligands (CA, NH4), 20 pockets (best druggability 0.85). MolNFT v2…

PDB: 8T2S
Type: protein + RNA
Length: 940 residues
Chains: 2
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.0
Source: [Eubacterium] rectale
Molecule: Group II intron reverse transcriptase/maturase; RNA (551-mer)
EC: 2.7.7.49
UniProt: A0A173ZME3
Ligands: CA, NH4
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · resolution 3.0 · 2 distinct chains · 56% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D	Group II intron reverse transcriptase/maturase (EC 2.7.7.49)	protein	389	56% helix, 9% strand	A0A173ZME3
B	RNA (551-mer)	rna	551	—	—

Ligands and binding sites

CA · Calcium ion · metal · 11 copies · chains B
NH4 · Ammonium ion · ion · 2 copies · chains B

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

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	835	0.85	0.89	84	CA
2	1180	0.68	0.74	58	empty
3	194	0.64	0.85	20	empty
4	723	0.63	0.74	39	empty
5	237	0.63	0.83	28	CA

Interfaces

1 interface between chains.

D–B · 3394 Å² buried · 85 hydrogen bonds · protein-nucleic

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 A0A173ZME3
Elsewhere: RCSB PDB 8T2S · PDBe 8T2S · UniProt A0A173ZME3

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