MolNFT v1 · #167806 · protein + DNA

Mycobacterium tuberculosis wt rnap transcription initiation intermediate structure with sorangicin

6VVX · DNA-directed RNA polymerase subunit alpha: “Mycobacterium tuberculosis wt rnap transcription initiation intermediate structure with sorangicin”. Electron microscopy, 3 ligands (SRN, ZN, MG), 20 pockets (best druggability 0.81).…

PDB: 6VVX
Type: protein + DNA
Length: 3,636 residues
Chains: 10
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, P9WJG2
Ligands: SRN, ZN, MG
Pockets: 20 · best druggability 0.81

Structure

electron microscopy · 10 distinct chains · 36% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	225	19% helix, 36% strand	A5U8D3
B	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	237	20% helix, 34% strand	A5U8D3
C	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	1111	25% helix, 23% strand	V9Z879
D	DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6)	protein	1266	43% helix, 13% strand	A5U053
E	DNA-directed RNA polymerase subunit omega (EC 2.7.7.6)	protein	83	43% helix, 5% strand	A0A0T9N9K3
F	RNA polymerase sigma factor siga	protein	319	67% helix, 2% strand	P9WGI0
J	RNA polymerase-binding protein rbpa	protein	108	23% helix, 19% strand	P9WHJ4
P	DNA (63-mer)	dna	63	—	—
M	RNA polymerase-binding transcription factor card	protein	159	49% helix, 16% strand	P9WJG2
O	DNA (65-mer)	dna	65	—	—

Ligands and binding sites

SRN · Sorangicin A · ligand · chains C, 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	725	0.81	0.84	86	empty
2	747	0.80	0.84	72	empty
3	1022	0.80	0.81	89	empty
4	376	0.78	0.88	44	empty
5	526	0.77	0.85	55	empty

Interfaces

25 interfaces between chains.

C–D · 8244 Å² buried · 80 hydrogen bonds · protein-protein
P–O · 2617 Å² buried · 216 hydrogen bonds · nucleic-nucleic
D–F · 2455 Å² buried · 27 hydrogen bonds · protein-protein
A–B · 2407 Å² buried · 7 hydrogen bonds · protein-protein
D–E · 2238 Å² buried · 26 hydrogen bonds · protein-protein

Compared structures

6VVX · Mycobacterium tuberculosis WT RNAP transcription initiation intermediate structure with… · the same entry in another collection · chain O against O, 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 0.97
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
Every structure of UniProt P9WJG2
Elsewhere: RCSB PDB 6VVX · PDBe 6VVX · UniProt A5U8D3 · UniProt V9Z879 · UniProt A5U053 · UniProt A0A0T9N9K3 · UniProt P9WGI0 · UniProt P9WHJ4 · UniProt P9WJG2

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