Research workbench

Escherichia COLI RNA polymerase promoter unwinding intermediate (trpo) with trar and rpst P2 promoter

Analyse Escherichia COLI RNA polymerase promoter unwinding intermediate (trpo) with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6PSW
Type: protein + DNA
Length: 3,955 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: P0A7Z4, P0A8V4, P0A8T7, P0A802, Q0P6L9, P41065
Ligands: 1N7, ZN, MG
Pockets: 20 · best druggability 0.82

Structure

electron microscopy · 10 distinct chains · 37% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
G	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	229	24% helix, 32% strand	P0A7Z4
H	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	219	19% helix, 35% strand	P0A7Z4
I	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	1341	29% helix, 21% strand	P0A8V4
J	DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6)	protein	1345	37% helix, 16% strand	P0A8T7
K	DNA-directed RNA polymerase subunit omega (EC 2.7.7.6)	protein	79	59% helix, 0% strand	P0A802
L	RNA polymerase sigma factor rpod	protein	473	66% helix, 1% strand	Q0P6L9
M	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	73	47% helix, 0% strand	P0A7Z4
N	Protein trar	protein	72	54% helix, 0% strand	P41065
O	DNA (85-mer)	dna	62	—	—
P	DNA (85-mer)	dna	62	—	—

Ligands and binding sites

1N7 · Chapso · ligand · 2 copies · chains G, I, J, L, P
ZN · Zinc ion · metal · 3 copies · chains J, N
MG · Magnesium ion · metal · chains J, N

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	988	0.82	0.84	106	empty
2	614	0.82	0.87	68	empty
3	445	0.81	0.89	52	empty
4	722	0.81	0.85	91	empty
5	407	0.80	0.89	52	empty

Interfaces

21 interfaces between chains.

I–J · 8181 Å² buried · 103 hydrogen bonds · protein-protein
J–L · 2807 Å² buried · 22 hydrogen bonds · protein-protein
I–L · 2279 Å² buried · 18 hydrogen bonds · protein-protein
O–P · 2201 Å² buried · 184 hydrogen bonds · nucleic-nucleic
G–I · 1978 Å² buried · 24 hydrogen bonds · protein-protein

Compared structures

6PSW · Escherichia coli RNA polymerase promoter unwinding intermediate (TRPo) with TraR and rpsT… · the same entry in another collection · chain P against P, TM-score 1.00
P0A802 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit omega (P0A802) · a predicted model of the same protein · chain K against A, TM-score 0.92
P41065 · AlphaFold monomer V2.0 prediction for protein trar (P41065) · a predicted model of the same protein · chain N against A, TM-score 0.78

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 P0A7Z4
Every structure of UniProt P0A8V4
Every structure of UniProt P0A8T7
Every structure of UniProt P0A802
Every structure of UniProt Q0P6L9
Every structure of UniProt P41065
Elsewhere: RCSB PDB 6PSW · PDBe 6PSW · UniProt P0A7Z4 · UniProt P0A8V4 · UniProt P0A8T7 · UniProt P0A802 · UniProt Q0P6L9 · UniProt P41065

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