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

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

PDB: 6ZCA
Type: protein
Length: 3,640 residues
Chains: 7
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Probable DNA-directed RNA polymerase subunit DELTA,PROBABLE DNA-directed RNA polymerase…
EC: 2.7.7.6, 3.6.4.12
UniProt: A0A0D1KIU7, A0A410WI33, A0A063XB83, A0A2J0WBQ0, A0A063XB23, A0A164TSE8
Ligands: ZN
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 7 distinct chains · 36% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D	Probable DNA-directed RNA polymerase subunit DELTA,PROBABLE DNA-directed RNA polymerase subunit DELTA,PROBABLE DNA-directed RNA polymerase subunit delta	protein	140	57% helix, 4% strand	A0A0D1KIU7
E	RNA polymerase subunit omega	protein	69	22% helix, 20% strand	A0A410WI33
U	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	231	26% helix, 28% strand	A0A063XB83
V	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	227	24% helix, 21% strand	A0A063XB83
X	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	1075	26% helix, 24% strand	A0A2J0WBQ0
Y	DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6)	protein	1127	41% helix, 10% strand	A0A063XB23
H	DNA helicase (EC 3.6.4.12)	protein	771	48% helix, 8% strand	A0A164TSE8

Ligands and binding sites

ZN · Zinc ion · metal · chains 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	835	0.85	0.88	115	empty
2	492	0.83	0.90	64	empty
3	696	0.82	0.86	87	empty
4	494	0.82	0.88	62	empty
5	1104	0.81	0.82	124	empty

Interfaces

14 interfaces between chains.

X–Y · 5166 Å² buried · 30 hydrogen bonds · protein-protein
Y–H · 4327 Å² buried · 38 hydrogen bonds · protein-protein
U–V · 1867 Å² buried · 5 hydrogen bonds · protein-protein
U–X · 1792 Å² buried · 17 hydrogen bonds · protein-protein
D–Y · 1346 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

6ZCA · Structure of the B. subtilis RNA POLYMERASE in complex with HelD (monomer) · 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 A0A0D1KIU7
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 6ZCA · PDBe 6ZCA · UniProt A0A0D1KIU7 · UniProt A0A410WI33 · UniProt A0A063XB83 · UniProt A0A2J0WBQ0 · UniProt A0A063XB23 · UniProt A0A164TSE8

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