MolNFT v2 · #218571 · protein

Plastid-encoded RNA polymerase

8R5O · DNA-directed RNA polymerase subunit alpha: “Plastid-encoded RNA polymerase”. Electron microscopy at 2.49, 3 ligands (SAH, FE, ZN), 20 pockets (best druggability 0.90). MolNFT v2 #218571 on GenesisL1: 3D structure, binding sites and…

PDB: 8R5O
Type: protein
Length: 6,679 residues
Chains: 20
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.49
Source: Sinapis alba
Molecule: DNA-directed RNA polymerase subunit alpha; DNA-directed RNA polymerase subunit beta…
EC: 2.7.7.6
UniProt: A0A6C0M610, A0A6C0M5W1, A0A6C0M5W0, A0A6C0M829
Ligands: SAH, FE, ZN
Pockets: 20 · best druggability 0.90

Structure

electron microscopy · resolution 2.49 · 20 distinct chains · 40% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-directed RNA polymerase subunit alpha	protein	301	32% helix, 31% strand	A0A6C0M610
B	DNA-directed RNA polymerase subunit alpha	protein	216	22% helix, 43% strand	A0A6C0M610
C	DNA-directed RNA polymerase subunit beta	protein	647	26% helix, 29% strand	A0A6C0M5W1
D	DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6)	protein	545	42% helix, 17% strand	A0A6C0M5W0
E	DNA-directed RNA polymerase subunit beta''	protein	912	32% helix, 22% strand	A0A6C0M829
F	PAP1	protein	537	61% helix, 0% strand	—
G	PAP2	protein	385	66% helix, 6% strand	—
H	PAP3	protein	440	43% helix, 14% strand	—
I	PAP4	protein	215	51% helix, 12% strand	—
J	PAP5	protein	234	46% helix, 3% strand	—
K	PAP6	protein	374	45% helix, 18% strand	—
L	PAP7	protein	408	42% helix, 18% strand	—
M	PAP8	protein	204	18% helix, 40% strand	—
N	PAP9	protein	215	53% helix, 12% strand	—
O	PAP10	protein	114	37% helix, 22% strand	—
P	PAP10	protein	108	39% helix, 23% strand	—
Q	PAP11	protein	220	39% helix, 19% strand	—
R	PAP12	protein	114	47% helix, 5% strand	—
S	FLN2	protein	386	38% helix, 17% strand	—
T	PTAC18	protein	104	14% helix, 47% strand	—

Ligands and binding sites

SAH · S-adenosyl-L-homocysteine · ligand · chains L, R
FE · Fe (III) ion · metal · 2 copies · chains I, N
ZN · Zinc ion · metal · chains E

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	1086	0.90	0.91	122	empty
2	783	0.86	0.89	74	empty
3	1025	0.85	0.86	101	empty
4	479	0.83	0.90	44	empty
5	444	0.82	0.90	55	empty

Interfaces

53 interfaces between chains.

E–H · 8424 Å² buried · 138 hydrogen bonds · protein-protein
D–E · 4490 Å² buried · 39 hydrogen bonds · protein-protein
C–E · 3673 Å² buried · 31 hydrogen bonds · protein-protein
C–J · 3387 Å² buried · 33 hydrogen bonds · protein-protein
A–S · 3123 Å² buried · 29 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

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 A0A6C0M610
Every structure of UniProt A0A6C0M5W1
Every structure of UniProt A0A6C0M5W0
Every structure of UniProt A0A6C0M829
Elsewhere: RCSB PDB 8R5O · PDBe 8R5O · UniProt A0A6C0M610 · UniProt A0A6C0M5W1 · UniProt A0A6C0M5W0 · UniProt A0A6C0M829

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