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The complete structure of the archaeal 13-subunit DNA-directed RNA polymerase

Analyse The complete structure of the archaeal 13-subunit DNA-directed RNA polymerase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2WAQ
Type: protein
Length: 3,334 residues
Chains: 13
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA-directed RNA polymerase RPO1N subunit; DNA-directed RNA polymerase RPO2 subunit…
Ligands: F3S, ZN, MG
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 13 distinct chains · 29% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-directed RNA polymerase RPO1N subunit	protein	841	34% helix, 14% strand	—
B	DNA-directed RNA polymerase RPO2 subunit	protein	1090	26% helix, 22% strand	—
C	DNA-directed RNA polymerase RPO1C subunit	protein	367	35% helix, 11% strand	—
D	DNA-directed RNA polymerase RPO3 subunit	protein	260	26% helix, 29% strand	—
E	DNA-directed RNA polymerase RPO7 subunit	protein	174	10% helix, 43% strand	—
F	DNA-directed RNA polymerase RPO4 subunit	protein	90	46% helix, 10% strand	—
G	DNA-directed RNA polymerase RPO8 subunit	protein	113	0% helix, 52% strand	—
H	DNA-directed RNA polymerase RPO5 subunit	protein	74	27% helix, 23% strand	—
K	DNA-directed RNA polymerase RPO6 subunit	protein	82	39% helix, 11% strand	—
L	DNA-directed RNA polymerase RPO11 subunit	protein	91	36% helix, 34% strand	—
N	DNA-directed RNA polymerase RPO10 subunit	protein	64	47% helix, 0% strand	—
P	DNA-directed RNA polymerase RPO12 subunit	protein	43	0% helix, 14% strand	—
Q	DNA-directed RNA polymerase RPO13 subunit	protein	45	49% helix, 0% strand	—

Ligands and binding sites

F3S · FE3-S4 cluster · ligand · chains D
ZN · Zinc ion · metal · 9 copies · chains A, C, B, N, P
MG · Magnesium ion · metal · chains A

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	1077	0.80	0.82	87	empty
2	1054	0.79	0.80	103	empty
3	1069	0.77	0.79	86	empty
4	1186	0.75	0.78	126	empty
5	83	0.74	0.97	18	empty

Interfaces

29 interfaces between chains.

A–B · 8361 Å² buried · 122 hydrogen bonds · protein-protein
A–C · 4759 Å² buried · 50 hydrogen bonds · protein-protein
E–F · 1943 Å² buried · 15 hydrogen bonds · protein-protein
D–L · 1716 Å² buried · 13 hydrogen bonds · protein-protein
B–D · 1694 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

2WAQ · The complete structure of the archaeal 13-subunit DNA-directed RNA Polymerase · the same entry in another collection · chain B against B, 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
Elsewhere: RCSB PDB 2WAQ · PDBe 2WAQ

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