MolNFT v1 · #120447 · protein + RNA

RNA dependent RNA polymerase ,VP4,DSRNA

5H0R · RNA-dependent RNA polymerase: “RNA dependent RNA polymerase ,VP4,DSRNA”. Electron microscopy, 20 pockets (best druggability 0.84). MolNFT v1 #120447 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5H0R
Type: protein + RNA
Length: 1,740 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA-dependent RNA polymerase; VP4 protein; RNA (42-mer)
UniProt: A0A0S1LIW6, Q80A92
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 4 distinct chains · 43% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
F	RNA-dependent RNA polymerase	protein	1183	44% helix, 10% strand	A0A0S1LIW6
G	VP4 protein	protein	473	42% helix, 10% strand	Q80A92
H	RNA (42-mer)	rna	42	—	—
I	RNA (42-mer)	rna	42	—	—

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	708	0.84	0.88	59	empty
2	505	0.84	0.90	71	empty
3	242	0.80	0.93	39	empty
4	83	0.76	0.98	21	empty
5	136	0.76	0.94	31	empty

Interfaces

4 interfaces between chains.

F–G · 3393 Å² buried · 42 hydrogen bonds · protein-protein
H–I · 1874 Å² buried · 174 hydrogen bonds · nucleic-nucleic
F–I · 401 Å² buried · 11 hydrogen bonds · protein-nucleic
F–H · 282 Å² buried · 4 hydrogen bonds · protein-nucleic

Compared structures

5H0R · RNA dependent RNA polymerase ,vp4,dsRNA · the same entry in another collection · chain H against H, 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 A0A0S1LIW6
Every structure of UniProt Q80A92
Elsewhere: RCSB PDB 5H0R · PDBe 5H0R · UniProt A0A0S1LIW6 · UniProt Q80A92

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