Research workbench

Structure of the apo-state of the bacteriophage phikz non-virion RNA polymerase

Analyse Structure of the apo-state of the bacteriophage phikz non-virion RNA polymerase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7OGR
Type: protein
Length: 1,775 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Unk helices; PHIKZ055,NON-virion DNA-dependent RNA polymerase subunit beta; PHIKZ068…
EC: 2.7.7.6
UniProt: Q8SDA7, A0A6H2A8Q1, Q8SD94, Q8SD91, I7DB36, Q8SD88, Q8SD39
Ligands: ZN
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 6 distinct chains · 34% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
X	Unk helices	protein	32	41% helix, 0% strand	—
A	PHIKZ055,NON-virion DNA-dependent RNA polymerase subunit beta	protein	190	32% helix, 18% strand	Q8SDA7, A0A6H2A8Q1
B	PHIKZ068	protein	197	51% helix, 6% strand	Q8SD94
C	PHIKZ071,DNA-directed RNA polymerase (EC 2.7.7.6)	protein	612	27% helix, 23% strand	Q8SD91, I7DB36
D	PHIKZ074	protein	373	41% helix, 6% strand	Q8SD88
E	PHIKZ123	protein	371	30% helix, 11% strand	Q8SD39

Ligands and binding sites

ZN · Zinc ion · metal · chains D

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	1183	0.84	0.85	97	empty
2	946	0.76	0.79	70	empty
3	101	0.68	0.91	18	empty
4	429	0.67	0.80	47	empty
5	566	0.64	0.76	69	empty

Interfaces

9 interfaces between chains.

C–E · 4007 Å² buried · 39 hydrogen bonds · protein-protein
A–D · 2986 Å² buried · 27 hydrogen bonds · protein-protein
C–D · 2296 Å² buried · 23 hydrogen bonds · protein-protein
A–C · 2184 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 1640 Å² buried · 17 hydrogen bonds · protein-protein

Compared structures

7OGR · Structure of the apo-state of the bacteriophage PhiKZ non-virion RNA polymerase · the same entry in another collection · chain X against X, 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 Q8SDA7
Every structure of UniProt A0A6H2A8Q1
Every structure of UniProt Q8SD94
Every structure of UniProt Q8SD91
Every structure of UniProt I7DB36
Every structure of UniProt Q8SD88
Every structure of UniProt Q8SD39
Elsewhere: RCSB PDB 7OGR · PDBe 7OGR · UniProt Q8SDA7 · UniProt A0A6H2A8Q1 · UniProt Q8SD94 · UniProt Q8SD91 · UniProt I7DB36 · UniProt Q8SD88 · UniProt Q8SD39

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