Research workbench

Structure of RPAP2-bound RNA polymerase II

Analyse Structure of RPAP2-bound RNA polymerase II in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7F4G
Type: protein
Length: 3,491 residues
Chains: 13
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RPB1; DNA-directed RNA polymerase subunit beta; DNA-directed RNA polymerase II subunit…
EC: 2.7.7.6
UniProt: A0A4X1TVZ5, I3LCH3, A0A4X1VTX4, A0A4X1VEK9, A0A4X1ULF2, P60899, A0A4X1UK25, A0A4X1TRS6, A0A481BYI6, A0A4X1VKG7
Ligands: ZN
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 13 distinct chains · 31% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RPB1	protein	1026	39% helix, 13% strand	—
B	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	978	27% helix, 23% strand	A0A4X1TVZ5
C	DNA-directed RNA polymerase II subunit RPB3	protein	254	22% helix, 28% strand	I3LCH3
E	DNA-directed RNA polymerase II subunit E	protein	208	36% helix, 20% strand	A0A4X1VTX4
F	DNA-directed RNA polymerase II subunit F	protein	76	34% helix, 14% strand	A0A4X1VEK9
H	DNA-directed RNA polymerases I, II, and III subunit RPABC3	protein	148	0% helix, 48% strand	A0A4X1ULF2
I	DNA-directed RNA polymerase II subunit RPB9	protein	114	4% helix, 31% strand	P60899
J	RPB10	protein	66	42% helix, 2% strand	—
K	RNA_POL_L_2 domain-containing protein	protein	115	39% helix, 23% strand	A0A4X1UK25
L	RPB12	protein	44	0% helix, 27% strand	A0A4X1TRS6
R	RPAP2	protein	163	50% helix, 6% strand	—
D	DNA-directed RNA polymerase II subunit RPB4	protein	128	57% helix, 2% strand	A0A481BYI6
G	DNA-directed RNA polymerase II subunit RPB7	protein	171	11% helix, 53% strand	A0A4X1VKG7

Ligands and binding sites

ZN · Zinc ion · metal · 5 copies · chains I, J, L, R

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	1181	0.87	0.88	125	empty
2	542	0.80	0.86	60	empty
3	917	0.80	0.82	106	empty
4	785	0.78	0.82	92	empty
5	1008	0.76	0.78	73	empty

Interfaces

26 interfaces between chains.

A–B · 3682 Å² buried · 32 hydrogen bonds · protein-protein
A–E · 2284 Å² buried · 28 hydrogen bonds · protein-protein
C–K · 2249 Å² buried · 13 hydrogen bonds · protein-protein
A–F · 2139 Å² buried · 20 hydrogen bonds · protein-protein
A–H · 2098 Å² buried · 25 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

7F4G · Structure of RPAP2-bound RNA polymerase II · the same entry in another collection · chain G against G, 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 A0A4X1TVZ5
Every structure of UniProt I3LCH3
Every structure of UniProt A0A4X1VTX4
Every structure of UniProt A0A4X1VEK9
Every structure of UniProt A0A4X1ULF2
Every structure of UniProt P60899
Every structure of UniProt A0A4X1UK25
Every structure of UniProt A0A4X1TRS6
Every structure of UniProt A0A481BYI6
Every structure of UniProt A0A4X1VKG7
Elsewhere: RCSB PDB 7F4G · PDBe 7F4G · UniProt A0A4X1TVZ5 · UniProt I3LCH3 · UniProt A0A4X1VTX4 · UniProt A0A4X1VEK9 · UniProt A0A4X1ULF2 · UniProt P60899 · UniProt A0A4X1UK25 · UniProt A0A4X1TRS6 · UniProt A0A481BYI6 · UniProt A0A4X1VKG7

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