MolNFT v1 · #144609 · protein

X-ray crystal structure of escherichia COLI RNA polymerase (rpob- H526Y) and ppapp complex

6BYU · DNA-directed RNA polymerase subunit alpha: “X-ray crystal structure of escherichia COLI RNA polymerase (rpob- H526Y) and ppapp complex”. X-ray diffraction, 3 ligands (ECJ, ZN, MG), 20 pockets (best druggability 0.84). MolNFT v1…

PDB: 6BYU
Type: protein
Length: 6,988 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: P0A7Z4, P0A8V2, P0A8T7, P0A800, P00579
Ligands: ECJ, ZN, MG
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 11 distinct chains · 40% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	228	21% helix, 37% strand	P0A7Z4
B	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	217	21% helix, 35% strand	P0A7Z4
C, I	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	1340	30% helix, 24% strand	P0A8V2
D	DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6)	protein	1163	42% helix, 14% strand	P0A8T7
E	DNA-directed RNA polymerase subunit omega (EC 2.7.7.6)	protein	89	63% helix, 0% strand	P0A800
F	RNA polymerase sigma factor rpod	protein	467	65% helix, 2% strand	P00579
G	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	224	21% helix, 37% strand	P0A7Z4
H	DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)	protein	217	21% helix, 35% strand	P0A7Z4
J	DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6)	protein	1155	42% helix, 14% strand	P0A8T7
K	DNA-directed RNA polymerase subunit omega (EC 2.7.7.6)	protein	79	63% helix, 0% strand	P0A800
L	RNA polymerase sigma factor rpod	protein	469	65% helix, 3% strand	P00579

Ligands and binding sites

ECJ · (5R)-5-(6-amino-9H-purin-9-yl)-2-({[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}methyl)-4-oxo-4,5-dihydrofuran-3-yl trihydrogen diphosphate · 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	1111	0.84	0.85	102	empty
2	643	0.83	0.87	69	empty
3	816	0.81	0.84	78	empty
4	719	0.80	0.84	72	empty
5	926	0.80	0.82	103	empty

Interfaces

19 interfaces between chains.

C–D · 8124 Å² buried · 108 hydrogen bonds · protein-protein
I–J · 8007 Å² buried · 104 hydrogen bonds · protein-protein
D–F · 2821 Å² buried · 26 hydrogen bonds · protein-protein
J–L · 2774 Å² buried · 25 hydrogen bonds · protein-protein
C–F · 2175 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 covalent (covalent ligand).

Compared structures

6BYU · X-ray crystal structure of Escherichia coli RNA polymerase (RpoB-H526Y) and ppApp complex · 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 P0A7Z4
Every structure of UniProt P0A8V2
Every structure of UniProt P0A8T7
Every structure of UniProt P0A800
Every structure of UniProt P00579
Elsewhere: RCSB PDB 6BYU · PDBe 6BYU · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0A800 · UniProt P00579

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