MolNFT v1 · #186971 · protein + DNA

Mycobacterium tuberculosis RNA polymerase sigma L holoenzyme open promoter complex containing tnp-2198

7RWI · DNA-directed RNA polymerase subunit alpha: “Mycobacterium tuberculosis RNA polymerase sigma L holoenzyme open promoter complex containing tnp-2198”. X-ray diffraction, 1 ligand (7US), 20 pockets (best druggability 0.86). MolNFT v1…

PDB: 7RWI
Type: protein + DNA
Length: 3,141 residues
Chains: 8
Method: x-ray diffraction
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, P9WGY8, A0A045J9E2, A0A045H2R3, A0A045IR27
Ligands: 7US
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 8 distinct chains · 36% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	225	21% helix, 40% strand	A5U8D3
B	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	232	22% helix, 38% strand	A5U8D3
C	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	1126	26% helix, 28% strand	P9WGY8
D	DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6)	protein	1264	45% helix, 14% strand	A0A045J9E2
E	DNA-directed RNA polymerase subunit omega (EC 2.7.7.6)	protein	81	46% helix, 1% strand	A0A045H2R3
F	RNA polymerase sigma factor	protein	174	73% helix, 2% strand	A0A045IR27
G	T DNA	dna	15	—	—
H	Nt DNA	dna	24	—	—

Ligands and binding sites

7US · (3am,9s,10bp,14s,15r,16s,17r,18r,19r,20s,21s,25r)-6,18, 20-trihydroxy-14-methoxy-7,9,15,17,19,21,25-heptamethyl-1'-[2-(2-methyl-5-nitro-1H-imidazol-1-yl) ethyl]-5,10,26-trioxo-3,5,9,10-tetrahydrospiro[9,4-(epoxypentadecanoimino)furo[2',3':7,8]naphtho[1,2-d]imidazole-2,4'-piperidin]-16-yl acetate · ligand · chains C, G

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	1001	0.86	0.87	103	empty
2	964	0.82	0.83	99	empty
3	786	0.80	0.84	69	empty
4	580	0.80	0.86	63	empty
5	1031	0.77	0.79	114	empty

Interfaces

16 interfaces between chains.

C–D · 8557 Å² buried · 109 hydrogen bonds · protein-protein
A–B · 2469 Å² buried · 19 hydrogen bonds · protein-protein
D–E · 2207 Å² buried · 28 hydrogen bonds · protein-protein
A–C · 2131 Å² buried · 30 hydrogen bonds · protein-protein
D–F · 2070 Å² buried · 25 hydrogen bonds · protein-protein

Compared structures

7RWI · Mycobacterium tuberculosis RNA polymerase sigma L holoenzyme open promoter complex… · the same entry in another collection · chain H against H, TM-score 1.00
P9WGY8 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta (P9WGY8) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 0.94

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 P9WGY8
Every structure of UniProt A0A045J9E2
Every structure of UniProt A0A045H2R3
Every structure of UniProt A0A045IR27
Elsewhere: RCSB PDB 7RWI · PDBe 7RWI · UniProt A5U8D3 · UniProt P9WGY8 · UniProt A0A045J9E2 · UniProt A0A045H2R3 · UniProt A0A045IR27

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.