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Structure of the B. subtilis RNA polymerase in complex with held (dimer)

Analyse Structure of the B. subtilis RNA polymerase in complex with held (dimer) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6ZFB
Type: protein
Length: 7,313 residues
Chains: 14
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA-directed RNA polymerase subunit delta; RNA polymerase subunit omega; DNA-directed RNA…
EC: 2.7.7.6, 3.6.4.12
UniProt: A0A410WI33, A0A063XB83, A0A2J0WBQ0, A0A063XB23, A0A164TSE8
Ligands: ZN
Pockets: 20 · best druggability 0.83

Structure

electron microscopy · 8 distinct chains · 34% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D, d	DNA-directed RNA polymerase subunit delta	protein	139	58% helix, 4% strand	—
E, e	RNA polymerase subunit omega	protein	69	23% helix, 28% strand	A0A410WI33
U, u	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	231	26% helix, 27% strand	A0A063XB83
V, v	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	227	23% helix, 21% strand	A0A063XB83
X	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	1093	26% helix, 24% strand	A0A2J0WBQ0
Y, y	DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6)	protein	1127	41% helix, 10% strand	A0A063XB23
H, h	DNA helicase (EC 3.6.4.12)	protein	771	49% helix, 8% strand	A0A164TSE8
x	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	1092	25% helix, 23% strand	A0A2J0WBQ0

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains Y, y

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	839	0.83	0.85	94	empty
2	1028	0.82	0.83	101	empty
3	678	0.81	0.85	92	empty
4	1064	0.81	0.82	105	empty
5	1135	0.81	0.82	101	empty

Interfaces

34 interfaces between chains.

x–y · 5689 Å² buried · 42 hydrogen bonds · protein-protein
X–Y · 5623 Å² buried · 40 hydrogen bonds · protein-protein
y–h · 4523 Å² buried · 32 hydrogen bonds · protein-protein
Y–H · 4484 Å² buried · 30 hydrogen bonds · protein-protein
u–v · 2026 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

6ZFB · Structure of the B. subtilis RNA POLYMERASE in complex with HelD (dimer) · the same entry in another collection · chain D against D, 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 A0A410WI33
Every structure of UniProt A0A063XB83
Every structure of UniProt A0A2J0WBQ0
Every structure of UniProt A0A063XB23
Every structure of UniProt A0A164TSE8
Elsewhere: RCSB PDB 6ZFB · PDBe 6ZFB · UniProt A0A410WI33 · UniProt A0A063XB83 · UniProt A0A2J0WBQ0 · UniProt A0A063XB23 · UniProt A0A164TSE8

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