MolNFT v1 · #160731 · protein + DNA

Escherichia COLI RNA polymerase promoter unwinding intermediate (TRPI2) with trar and rpst P2 promoter

6PSU · Protein trar: “Escherichia COLI RNA polymerase promoter unwinding intermediate (TRPI2) with trar and rpst P2 promoter”. Electron microscopy, 3 ligands (1N7, ZN, MG), 20 pockets (best druggability 0.85). MolNFT v1 #160731 on…

PDB: 6PSU
Type: protein + DNA
Length: 3,956 residues
Chains: 10
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein trar; DNA-directed RNA polymerase subunit alpha; DNA-directed RNA polymerase…
EC: 2.7.7.6
UniProt: P41065, P0A7Z4, P0A8V4, P0A8T7, P0A802, Q0P6L9
Ligands: 1N7, ZN, MG
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 10 distinct chains · 36% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
N	Protein trar	protein	72	56% helix, 6% strand	P41065
G	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	230	22% helix, 30% strand	P0A7Z4
H	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	217	21% helix, 25% strand	P0A7Z4
I	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	1340	29% helix, 19% strand	P0A8V4
J	DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6)	protein	1344	35% helix, 13% strand	P0A8T7
K	DNA-directed RNA polymerase subunit omega (EC 2.7.7.6)	protein	72	57% helix, 0% strand	P0A802
L	RNA polymerase sigma factor rpod	protein	529	62% helix, 1% strand	Q0P6L9
O	DNA (85-mer)	dna	42	—	—
P	DNA (85-mer)	dna	37	—	—
M	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	73	51% helix, 0% strand	P0A7Z4

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	994	0.85	0.86	100	empty
2	980	0.79	0.81	94	empty
3	1023	0.79	0.81	96	empty
4	565	0.79	0.85	75	empty
5	830	0.78	0.81	83	empty

Interfaces

20 interfaces between chains.

I–J · 8138 Å² buried · 103 hydrogen bonds · protein-protein
J–L · 3228 Å² buried · 31 hydrogen bonds · protein-protein
I–L · 2394 Å² buried · 20 hydrogen bonds · protein-protein
G–H · 2026 Å² buried · 12 hydrogen bonds · protein-protein
G–I · 1862 Å² buried · 27 hydrogen bonds · protein-protein

Compared structures

6PSU · Escherichia coli RNA polymerase promoter unwinding intermediate (TRPi2) with TraR and… · the same entry in another collection · chain M against M, 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 0.80

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 6PSU · PDBe 6PSU · UniProt P41065 · UniProt P0A7Z4 · UniProt P0A8V4 · UniProt P0A8T7 · UniProt P0A802 · UniProt Q0P6L9

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