Research workbench

Single particle cryo EM structure of mycobacterium tuberculosis RNA polymerase in complex with fidaxomicin

Analyse Single particle cryo EM structure of mycobacterium tuberculosis RNA polymerase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6FBV
Type: protein
Length: 3,217 residues
Chains: 6
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA-directed RNA polymerase subunit alpha; DNA-directed RNA polymerase subunit beta…
EC: 2.7.7.6
UniProt: P9WGZ1, P9WGY9, P9WGY7, P9WGY5, P9WGI1
Ligands: FI8, ZN, MG
Pockets: 20 · best druggability 0.82

Structure

electron microscopy · 6 distinct chains · 36% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	223	21% helix, 38% strand	P9WGZ1
B	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	230	22% helix, 37% strand	P9WGZ1
C	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	1118	26% helix, 26% strand	P9WGY9
D	DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6)	protein	1270	43% helix, 14% strand	P9WGY7
E	DNA-directed RNA polymerase subunit omega (EC 2.7.7.6)	protein	83	46% helix, 5% strand	P9WGY5
F	RNA polymerase sigma factor siga	protein	293	66% helix, 1% strand	P9WGI1

Ligands and binding sites

FI8 · Fidaxomicin · ligand · chains C, D, F
ZN · Zinc ion · metal · 2 copies · chains D
MG · Magnesium 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, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	675	0.82	0.87	89	empty
2	808	0.79	0.82	92	empty
3	707	0.77	0.82	80	empty
4	517	0.76	0.84	46	FI8
5	356	0.76	0.86	36	empty

Interfaces

10 interfaces between chains.

C–D · 7921 Å² buried · 83 hydrogen bonds · protein-protein
D–F · 2478 Å² buried · 30 hydrogen bonds · protein-protein
A–B · 2298 Å² buried · 8 hydrogen bonds · protein-protein
D–E · 2232 Å² buried · 22 hydrogen bonds · protein-protein
A–C · 1879 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

6FBV · Single particle cryo em structure of Mycobacterium tuberculosis RNA polymerase in complex… · the same entry in another collection · chain F against F, TM-score 1.00
P9WGY9 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta (P9WGY9) · a predicted model of the same protein · chain C against A, TM-score 0.98
P9WGY7 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta' (P9WGY7) · a predicted model of the same protein · chain D against A, TM-score 0.95
P9WGY5 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit omega (P9WGY5) · a predicted model of the same protein · chain E against A, TM-score 0.92
P9WGI1 · AlphaFold monomer V2.0 prediction for RNA polymerase sigma factor siga (P9WGI1) · a predicted model of the same protein · chain F against A, TM-score 0.82

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 P9WGZ1
Every structure of UniProt P9WGY9
Every structure of UniProt P9WGY7
Every structure of UniProt P9WGY5
Every structure of UniProt P9WGI1
Elsewhere: RCSB PDB 6FBV · PDBe 6FBV · UniProt P9WGZ1 · UniProt P9WGY9 · UniProt P9WGY7 · UniProt P9WGY5 · UniProt P9WGI1

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