MolNFT v1 · #111067 · protein

Escherichia COLI RNA polymerase in complex with squaramide compound 14 (N-[3,4-dioxo-2-(4-{[4-(TRIFLUOROMETHYL)BENZYL]AMINO}PIPERIDIN-1-yl) cyclobut-1-en-1-yl]-3,5-dimethyl-1,2-oxazole-4-sulfonamide)

4YFN · DNA-directed RNA polymerase subunit alpha: “Escherichia COLI RNA polymerase in complex with squaramide compound 14…”. X-ray diffraction, 3 ligands (4C2, ZN, MG), 20 pockets (best druggability 0.84). MolNFT v1 #111067 on GenesisL1…

PDB: 4YFN
Type: protein
Length: 7,067 residues
Chains: 12
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: A7ZSI4, A7ZUK1, A7ZUK2, A7ZTK1, P00579
Ligands: 4C2, ZN, MG
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 11 distinct chains · 40% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	235	21% helix, 36% strand	A7ZSI4
B	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	289	25% helix, 29% strand	A7ZSI4
C, I	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	1340	30% helix, 24% strand	A7ZUK1
D	DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6)	protein	1163	42% helix, 14% strand	A7ZUK2
E	DNA-directed RNA polymerase subunit omega (EC 2.7.7.6)	protein	89	63% helix, 0% strand	A7ZTK1
F	RNA polymerase sigma factor rpod	protein	468	68% helix, 3% strand	P00579
G	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	227	19% helix, 39% strand	A7ZSI4
H	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	216	18% helix, 39% strand	A7ZSI4
J	DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6)	protein	1152	42% helix, 13% strand	A7ZUK2
K	DNA-directed RNA polymerase subunit omega (EC 2.7.7.6)	protein	79	57% helix, 0% strand	A7ZTK1
L	RNA polymerase sigma factor rpod	protein	469	65% helix, 3% strand	P00579

Ligands and binding sites

4C2 · N-[3,4-dioxo-2-(4-{[4-(trifluoromethyl)benzyl]amino}piperidin-1-yl)cyclobut-1-en-1-yl]-3,5-dimethyl-1,2-oxazole-4-sulfonamide · ligand · 2 copies · chains C, D, I, J
ZN · Zinc ion · metal · 4 copies · chains D, J
MG · Magnesium ion · metal · 2 copies · chains D, 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	1163	0.84	0.85	111	empty
2	921	0.83	0.85	78	empty
3	1189	0.81	0.82	88	4C2
4	1146	0.81	0.82	90	4C2
5	900	0.80	0.83	92	empty

Interfaces

20 interfaces between chains.

C–D · 7957 Å² buried · 104 hydrogen bonds · protein-protein
I–J · 7884 Å² buried · 95 hydrogen bonds · protein-protein
J–L · 2770 Å² buried · 22 hydrogen bonds · protein-protein
D–F · 2757 Å² buried · 23 hydrogen bonds · protein-protein
A–B · 2199 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

4YFN · Escherichia coli RNA polymerase in complex with squaramide compound 14… · the same entry in another collection · chain L against L, TM-score 1.00

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 A7ZSI4
Every structure of UniProt A7ZUK1
Every structure of UniProt A7ZUK2
Every structure of UniProt A7ZTK1
Every structure of UniProt P00579
Elsewhere: RCSB PDB 4YFN · PDBe 4YFN · UniProt A7ZSI4 · UniProt A7ZUK1 · UniProt A7ZUK2 · UniProt A7ZTK1 · UniProt P00579

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