MolNFT v1 · #52781 · protein

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

2WB1 · DNA-directed RNA polymerase RPO1N subunit: “The complete structure of the archaeal 13-subunit DNA- directed RNA polymerase”. X-ray diffraction, 3 ligands (F3S, ZN, MG), 20 pockets (best druggability 0.81). MolNFT v1 #52781 on…

PDB: 2WB1
Type: protein
Length: 6,645 residues
Chains: 26
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 0.81

Structure

x-ray diffraction · 14 distinct chains · 29% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, W	DNA-directed RNA polymerase RPO1N subunit	protein	841	36% helix, 14% strand	—
B, R	DNA-directed RNA polymerase RPO2 subunit	protein	1090	25% helix, 22% strand	—
C, Y	DNA-directed RNA polymerase RPO1C subunit	protein	367	38% helix, 11% strand	—
D, S	DNA-directed RNA POLYMERASERPO3 subunit	protein	260	25% helix, 30% strand	—
E, T	DNA-directed RNA polymerase RPO7 subunit	protein	174	10% helix, 44% strand	—
F, U	DNA-directed RNA polymerase RPO4 subunit	protein	90	42% helix, 10% strand	—
G, V	DNA-directed RNA polymerase RPO8 subunit	protein	113	0% helix, 52% strand	—
H, Z	DNA-directed RNA polymerase RPO5 subunit	protein	74	26% helix, 16% strand	—
I, K	DNA-directed RNA polymerase RPO6 subunit	protein	82	38% helix, 9% strand	—
J	DNA-directed RNA polymerase RPO13 subunit	protein	35	46% helix, 0% strand	—
L, M	DNA-directed RNA polymerase RPO11 subunit	protein	91	36% helix, 30% strand	—
N, O	DNA-directed RNA polymerase RPO10 subunit	protein	64	44% helix, 0% strand	—
P, X	DNA-directed RNA polymerase RPO12 subunit	protein	43	0% helix, 19% strand	—
Q	DNA-directed RNA polymerase RPO13 subunit	protein	32	56% helix, 0% strand	—

Ligands and binding sites

F3S · FE3-S4 cluster · ligand · 2 copies · chains D, S
ZN · Zinc ion · metal · 10 copies · chains A, B, N, O, P, R, W, X
MG · Magnesium ion · metal · 2 copies · chains A, W

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	1021	0.81	0.82	117	empty
2	978	0.79	0.81	85	empty
3	1066	0.78	0.80	105	empty
4	1024	0.77	0.79	88	empty
5	1134	0.75	0.78	88	empty

Interfaces

67 interfaces between chains.

R–W · 8389 Å² buried · 119 hydrogen bonds · protein-protein
A–B · 8271 Å² buried · 102 hydrogen bonds · protein-protein
W–Y · 4878 Å² buried · 50 hydrogen bonds · protein-protein
A–C · 4821 Å² buried · 47 hydrogen bonds · protein-protein
E–F · 1960 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

2WB1 · The complete structure of the archaeal 13-subunit DNA-directed 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
Elsewhere: RCSB PDB 2WB1 · PDBe 2WB1

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