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Crystal structure of cbr 9393 bound to escherichia COLI RNA polymerase holoenzyme

Analyse Crystal structure of cbr 9393 bound to escherichia COLI RNA polymerase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4XSZ
Type: protein
Length: 7,078 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, B1IYV1, P00579
Ligands: 42U, ZN, MG
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 11 distinct chains · 39% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	224	21% helix, 35% strand	A7ZSI4
B	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	220	18% helix, 30% strand	A7ZSI4
C, I	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	1340	29% helix, 23% strand	A7ZUK1
D	DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6)	protein	1166	42% helix, 14% strand	A7ZUK2
E	DNA-directed RNA polymerase subunit omega (EC 2.7.7.6)	protein	89	67% helix, 0% strand	B1IYV1
F	RNA polymerase sigma factor rpod	protein	470	64% helix, 3% strand	P00579
G	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	228	20% helix, 35% strand	A7ZSI4
H	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	217	18% helix, 31% strand	A7ZSI4
J	DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6)	protein	1236	39% helix, 15% strand	A7ZUK2
K	DNA-directed RNA polymerase subunit omega (EC 2.7.7.6)	protein	79	61% helix, 0% strand	B1IYV1
L	RNA polymerase sigma factor rpod	protein	469	65% helix, 3% strand	P00579

Ligands and binding sites

42U · 4-[3-(4-fluorophenyl)-1H-pyrazol-4-yl]-N-[2-(piperazin-1-yl)ethyl]-2-(trifluoromethyl)aniline · 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	593	0.82	0.87	70	empty
2	578	0.82	0.87	67	empty
3	1030	0.81	0.82	105	empty
4	848	0.79	0.82	81	empty
5	578	0.78	0.84	52	empty

Interfaces

19 interfaces between chains.

I–J · 8134 Å² buried · 110 hydrogen bonds · protein-protein
C–D · 8108 Å² buried · 110 hydrogen bonds · protein-protein
J–L · 2826 Å² buried · 29 hydrogen bonds · protein-protein
D–F · 2816 Å² buried · 29 hydrogen bonds · protein-protein
C–F · 2122 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

4XSZ · Crystal structure of CBR 9393 bound to Escherichia coli RNA polymerase holoenzyme · 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 B1IYV1
Every structure of UniProt P00579
Elsewhere: RCSB PDB 4XSZ · PDBe 4XSZ · UniProt A7ZSI4 · UniProt A7ZUK1 · UniProt A7ZUK2 · UniProt B1IYV1 · UniProt P00579

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