Research workbench

Mycobacterium tuberculosis rnap with RBPA/US fork and corallopyronin

Analyse Mycobacterium tuberculosis rnap with RBPA/US fork and corallopyronin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6M7J
Type: protein + DNA
Length: 3,406 residues
Chains: 9
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: A5U8D3, V9Z879, A5U053, A0A0T9N9K3, P9WGI0, P9WHJ4
Ligands: C0L, ZN, MG
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 9 distinct chains · 37% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	225	20% helix, 33% strand	A5U8D3
B	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	237	19% helix, 29% strand	A5U8D3
C	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	1111	26% helix, 22% strand	V9Z879
D	DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6)	protein	1266	45% helix, 11% strand	A5U053
E	DNA-directed RNA polymerase subunit omega (EC 2.7.7.6)	protein	83	48% helix, 5% strand	A0A0T9N9K3
F	RNA polymerase sigma factor siga	protein	319	70% helix, 2% strand	P9WGI0
J	RNA polymerase-binding protein rbpa	protein	108	26% helix, 21% strand	P9WHJ4
O	DNA (31-mer)	dna	31	—	—
P	DNA (26-mer)	dna	26	—	—

Ligands and binding sites

C0L · Methyl [(1E,5R)-5-{(3E)-3-[(2E,4E,8R,9E,12E)-1,8-dihydroxy-2,5,9-trimethyltetradeca-2,4,9,12-tetraen-1-ylidene]-2,4-dioxo-3,4-dihydro-2H-pyran-6-yl}hex-1-en-1-yl]carbamate · ligand · chains C, D
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	878	0.86	0.87	100	C0L
2	849	0.84	0.86	127	empty
3	798	0.81	0.84	101	empty
4	151	0.80	0.95	34	empty
5	421	0.79	0.87	67	empty

Interfaces

19 interfaces between chains.

C–D · 7722 Å² buried · 86 hydrogen bonds · protein-protein
A–B · 2167 Å² buried · 11 hydrogen bonds · protein-protein
D–E · 2136 Å² buried · 30 hydrogen bonds · protein-protein
D–F · 2102 Å² buried · 28 hydrogen bonds · protein-protein
A–C · 1827 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

6M7J · Mycobacterium tuberculosis RNAP with RbpA/us fork and Corallopyronin · the same entry in another collection · chain P against P, TM-score 1.00
A5U053 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta' (A5U053) · a predicted model of the same protein · chain D against A, TM-score 0.96
A5U8D3 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit alpha (A5U8D3) · a predicted model of the same protein · chain A against A, TM-score 0.93

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 A5U8D3
Every structure of UniProt V9Z879
Every structure of UniProt A5U053
Every structure of UniProt A0A0T9N9K3
Every structure of UniProt P9WGI0
Every structure of UniProt P9WHJ4
Elsewhere: RCSB PDB 6M7J · PDBe 6M7J · UniProt A5U8D3 · UniProt V9Z879 · UniProt A5U053 · UniProt A0A0T9N9K3 · UniProt P9WGI0 · UniProt P9WHJ4

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