MolNFT v1 · #177791 · protein + DNA + RNA

The cryo-EM structure of a. thaliana pol IV-RDR2 backtracked complex

7EU0 · DNA-directed RNA polymerase IV subunit 1: “The cryo-EM structure of a. thaliana pol IV-RDR2 backtracked complex”. Electron microscopy, 2 ligands (ZN, MG), 20 pockets (best druggability 0.89). MolNFT v1 #177791 on GenesisL1: 3D…

PDB: 7EU0
Type: protein + DNA + RNA
Length: 4,249 residues
Chains: 15
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA-directed RNA polymerase IV subunit 1; DNA-directed RNA polymerases IV and V subunit…
EC: 2.7.7.6, 2.7.7.48
UniProt: Q9LK40, Q39211, O81098, Q9FJ98, Q9M1A8, Q6NLH0, Q8LFJ6, Q38859, Q9FLM8, O82504
Ligands: ZN, MG
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · 15 distinct chains · 27% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-directed RNA polymerase IV subunit 1	protein	1060	33% helix, 16% strand	—
B	DNA-directed RNA polymerases IV and V subunit 2 (EC 2.7.7.6)	protein	1054	25% helix, 22% strand	Q9LK40
C	DNA-directed RNA polymerases II, IV and V subunit 3	protein	291	21% helix, 31% strand	Q39211
E	DNA-directed RNA polymerases II and IV subunit 5A	protein	198	32% helix, 20% strand	O81098
F	DNA-directed RNA polymerases II, IV and V subunit 6A	protein	76	36% helix, 16% strand	Q9FJ98
H	DNA-directed RNA polymerases II, IV and V subunit 8B	protein	126	0% helix, 40% strand	Q9M1A8
I	DNA-directed RNA polymerases II, IV and V subunit 9A	protein	113	0% helix, 37% strand	Q6NLH0
J	DNA-directed RNA polymerases II, IV and V subunit 10	protein	62	47% helix, 5% strand	Q8LFJ6
K	DNA-directed RNA polymerases II, IV and V subunit 11	protein	94	40% helix, 27% strand	Q38859
L	DNA-directed RNA polymerases II, IV and V subunit 12	protein	42	0% helix, 33% strand	Q9FLM8
M	RNA-dependent RNA polymerase 2 (EC 2.7.7.48)	protein	1052	28% helix, 20% strand	O82504
N	DNA (5'- D(CPTPGPTPGPCPTPTPAPTPCPGPGPTPAPGPAPGPTPG)-3')	dna	17	—	—
O	RNA (39-mer)	rna	32	—	—
Q	DNA (33-mer)	dna	28	—	—
R	RNA (5'-R(CPCPGPA)-3')	rna	4	—	—

Ligands and binding sites

ZN · Zinc ion · metal · 8 copies · chains A, B, C, I, J, L
MG · Magnesium ion · metal · 2 copies · chains A, O, M, R

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

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	1044	0.89	0.90	133	empty
2	826	0.87	0.90	109	empty
3	978	0.86	0.87	92	empty
4	1149	0.79	0.80	115	empty
5	829	0.77	0.81	72	empty

Interfaces

34 interfaces between chains.

A–B · 8046 Å² buried · 82 hydrogen bonds · protein-protein
A–I · 2390 Å² buried · 22 hydrogen bonds · protein-protein
C–K · 1882 Å² buried · 13 hydrogen bonds · protein-protein
A–E · 1653 Å² buried · 17 hydrogen bonds · protein-protein
B–J · 1476 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

7EU0 · The cryo-EM structure of A. thaliana Pol IV-RDR2 backtracked complex · the same entry in another collection · chain M against M, TM-score 1.00

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 Q9LK40
Every structure of UniProt Q39211
Every structure of UniProt O81098
Every structure of UniProt Q9FJ98
Every structure of UniProt Q9M1A8
Every structure of UniProt Q6NLH0
Every structure of UniProt Q8LFJ6
Every structure of UniProt Q38859
Every structure of UniProt Q9FLM8
Every structure of UniProt O82504
Elsewhere: RCSB PDB 7EU0 · PDBe 7EU0 · UniProt Q9LK40 · UniProt Q39211 · UniProt O81098 · UniProt Q9FJ98 · UniProt Q9M1A8 · UniProt Q6NLH0 · UniProt Q8LFJ6 · UniProt Q38859 · UniProt Q9FLM8 · UniProt O82504

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.