Research workbench

RNA polymerase II dimer (class 3)

Analyse RNA polymerase II dimer (class 3) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7OZP
Type: protein
Length: 6,774 residues
Chains: 24
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA-directed RNA polymerase subunit; DNA-directed RNA polymerase subunit beta…
EC: 2.7.7.6
UniProt: A0A0B8RVL1, A0A481DF93, A0A287ADR4, I3LSI7, F1SKN8, I3LJZ9, A0A4X1ULF2, P60899, A0A7K6NXI9, A0A4X1UK25, I3LN51
Ligands: ZN
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 12 distinct chains · 33% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, M	DNA-directed RNA polymerase subunit (EC 2.7.7.6)	protein	1033	44% helix, 14% strand	—
B, N	DNA-directed RNA polymerase subunit beta (EC 2.7.7.6)	protein	1023	31% helix, 24% strand	A0A0B8RVL1
C, O	DNA-directed RNA polymerase II subunit RPB3	protein	257	25% helix, 27% strand	A0A481DF93
D, P	RNA polymerase II subunit D	protein	129	61% helix, 3% strand	A0A287ADR4
E, Q	DNA-directed RNA polymerase II subunit E	protein	209	37% helix, 23% strand	I3LSI7
F, R	DNA-directed RNA polymerase II subunit F	protein	79	34% helix, 16% strand	F1SKN8
G, S	DNA-directed RNA polymerase II subunit RPB7	protein	171	9% helix, 51% strand	I3LJZ9
H, T	DNA-directed RNA polymerases I, II, and III subunit RPABC3	protein	148	0% helix, 48% strand	A0A4X1ULF2
I, U	DNA-directed RNA polymerase II subunit RPB9	protein	114	8% helix, 28% strand	P60899
J, V	DNA-directed RNA polymerases I, II, and III subunit RPABC5	protein	65	48% helix, 3% strand	A0A7K6NXI9
K, W	RNA_POL_L_2 domain-containing protein	protein	115	45% helix, 22% strand	A0A4X1UK25
L, X	RNA polymerase II subunit K	protein	44	0% helix, 27% strand	I3LN51

Ligands and binding sites

ZN · Zinc ion · metal · 10 copies · chains C, I, J, L, O, U, V, X

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	1134	0.87	0.88	119	empty
2	1113	0.87	0.88	115	empty
3	731	0.83	0.87	91	empty
4	688	0.83	0.87	88	empty
5	691	0.82	0.86	94	empty

Interfaces

53 interfaces between chains.

M–N · 4148 Å² buried · 47 hydrogen bonds · protein-protein
A–B · 4131 Å² buried · 47 hydrogen bonds · protein-protein
M–Q · 2390 Å² buried · 28 hydrogen bonds · protein-protein
A–E · 2388 Å² buried · 28 hydrogen bonds · protein-protein
C–K · 2301 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

P60899 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase II subunit RPB9 (P60899) · a predicted model of the same protein · chain I against A, TM-score 0.83

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 A0A0B8RVL1
Every structure of UniProt A0A481DF93
Every structure of UniProt A0A287ADR4
Every structure of UniProt I3LSI7
Every structure of UniProt F1SKN8
Every structure of UniProt I3LJZ9
Every structure of UniProt A0A4X1ULF2
Every structure of UniProt P60899
Every structure of UniProt A0A7K6NXI9
Every structure of UniProt A0A4X1UK25
Every structure of UniProt I3LN51
Elsewhere: RCSB PDB 7OZP · PDBe 7OZP · UniProt A0A0B8RVL1 · UniProt A0A481DF93 · UniProt A0A287ADR4 · UniProt I3LSI7 · UniProt F1SKN8 · UniProt I3LJZ9 · UniProt A0A4X1ULF2 · UniProt P60899 · UniProt A0A7K6NXI9 · UniProt A0A4X1UK25 · UniProt I3LN51

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