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Escherichia COLI RNA polymerase promoter unwinding intermediate (TRPI1.5B) with trar and mutant rpst P2 promoter

Analyse Escherichia COLI RNA polymerase promoter unwinding intermediate (TRPI1.5B) with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6PST
Type: protein + DNA
Length: 3,827 residues
Chains: 10
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein trar; DNA (85-mer); DNA-directed RNA polymerase subunit alpha; DNA-directed RNA…
EC: 2.7.7.6
UniProt: P41065, P0A7Z4, P0A8V4, P0A8T7, P0A802, Q0P6L9
Ligands: 1N7, ZN, MG
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 10 distinct chains · 39% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
N	Protein trar	protein	72	54% helix, 0% strand	P41065
O	DNA (85-mer)	dna	50	—	—
P	DNA (85-mer)	dna	51	—	—
M	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	73	44% helix, 0% strand	P0A7Z4
G	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	232	22% helix, 40% strand	P0A7Z4
H	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	218	20% helix, 37% strand	P0A7Z4
I	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	1337	29% helix, 23% strand	P0A8V4
J	DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6)	protein	1164	41% helix, 16% strand	P0A8T7
K	DNA-directed RNA polymerase subunit omega (EC 2.7.7.6)	protein	72	68% helix, 0% strand	P0A802
L	RNA polymerase sigma factor rpod	protein	558	66% helix, 1% strand	Q0P6L9

Ligands and binding sites

1N7 · Chapso · ligand · 4 copies · chains N, J, G, I, L
ZN · Zinc ion · metal · 3 copies · chains N, J
MG · Magnesium ion · metal · chains J

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	1042	0.84	0.85	92	empty
2	835	0.79	0.82	117	MG
3	1079	0.77	0.79	90	empty
4	491	0.76	0.85	56	empty
5	124	0.76	0.95	28	empty

Interfaces

21 interfaces between chains.

I–J · 8173 Å² buried · 97 hydrogen bonds · protein-protein
J–L · 3898 Å² buried · 32 hydrogen bonds · protein-protein
I–L · 2561 Å² buried · 23 hydrogen bonds · protein-protein
G–H · 2181 Å² buried · 16 hydrogen bonds · protein-protein
O–P · 2094 Å² buried · 161 hydrogen bonds · nucleic-nucleic

Compared structures

6PST · Escherichia coli RNA polymerase promoter unwinding intermediate (TRPi1.5b) with TraR and… · the same entry in another collection · chain L against L, 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 0.96
P41065 · AlphaFold monomer V2.0 prediction for protein trar (P41065) · a predicted model of the same protein · chain N against A, TM-score 0.77

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 P41065
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
Elsewhere: RCSB PDB 6PST · PDBe 6PST · UniProt P41065 · UniProt P0A7Z4 · UniProt P0A8V4 · UniProt P0A8T7 · UniProt P0A802 · UniProt Q0P6L9

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