MolNFT v1 · #110317 · protein

Crystal structure of cbr 9379 bound to escherichia COLI RNA polymerase holoenzyme

4XSY · DNA-directed RNA polymerase subunit alpha: “Crystal structure of cbr 9379 bound to escherichia COLI RNA polymerase holoenzyme”. X-ray diffraction, 3 ligands (42T, ZN, MG), 20 pockets (best druggability 0.83). MolNFT v1 #110317 on…

PDB: 4XSY
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, A8ARN6, P00579
Ligands: 42T, ZN, MG
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 11 distinct chains · 40% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	224	18% helix, 33% strand	A7ZSI4
B	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	220	18% helix, 25% strand	A7ZSI4
C, I	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	1340	31% helix, 22% strand	A7ZUK1
D	DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6)	protein	1166	43% helix, 13% strand	A7ZUK2
E	DNA-directed RNA polymerase subunit omega (EC 2.7.7.6)	protein	89	66% helix, 0% strand	A8ARN6
F	RNA polymerase sigma factor rpod	protein	470	66% helix, 3% strand	P00579
G	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	228	18% helix, 32% strand	A7ZSI4
H	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	217	18% helix, 29% strand	A7ZSI4
J	DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6)	protein	1236	40% helix, 15% strand	A7ZUK2
K	DNA-directed RNA polymerase subunit omega (EC 2.7.7.6)	protein	79	61% helix, 0% strand	A8ARN6
L	RNA polymerase sigma factor rpod	protein	469	65% helix, 3% strand	P00579

Ligands and binding sites

42T · 3-{[(2,6-dichlorophenyl)carbamoyl]amino}-N-hydroxy-N'-phenyl-5-(trifluoromethyl)benzenecarboximidamide · 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	656	0.83	0.87	79	empty
2	1195	0.82	0.83	124	empty
3	579	0.81	0.87	65	empty
4	1176	0.78	0.80	95	empty
5	559	0.78	0.84	60	empty

Interfaces

19 interfaces between chains.

I–J · 8165 Å² buried · 104 hydrogen bonds · protein-protein
C–D · 8135 Å² buried · 104 hydrogen bonds · protein-protein
D–F · 2819 Å² buried · 29 hydrogen bonds · protein-protein
J–L · 2811 Å² buried · 30 hydrogen bonds · protein-protein
C–F · 2069 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

4XSY · Crystal structure of CBR 9379 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 A8ARN6
Every structure of UniProt P00579
Elsewhere: RCSB PDB 4XSY · PDBe 4XSY · UniProt A7ZSI4 · UniProt A7ZUK1 · UniProt A7ZUK2 · UniProt A8ARN6 · UniProt P00579

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