MolNFT v1 · #146761 · protein

RNA pol II(G)

6DRD · DNA-directed RNA polymerase II subunit RPB1: “RNA pol II(G)”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.87). MolNFT v1 #146761 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6DRD
Type: protein
Length: 3,349 residues
Chains: 13
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA-directed RNA polymerase II subunit RPB1; DNA-directed RNA polymerase II subunit RPB2…
EC: 2.7.7.6, 2.7.7.48
UniProt: P24928, P30876, P19387, O15514, P19388, P61218, P62487, P52434, P36954, P62875, P52435, P53803, P0CAP2
Ligands: ZN
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 13 distinct chains · 24% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-directed RNA polymerase II subunit RPB1 (EC 2.7.7.6, 2.7.7.48)	protein	1000	33% helix, 11% strand	P24928
B	DNA-directed RNA polymerase II subunit RPB2 (EC 2.7.7.6)	protein	1009	20% helix, 19% strand	P30876
C	DNA-directed RNA polymerase II subunit RPB3	protein	262	19% helix, 24% strand	P19387
D	DNA-directed RNA polymerase II subunit RPB4	protein	128	50% helix, 1% strand	O15514
E	DNA-directed RNA polymerases I, II, and III subunit RPABC1	protein	185	27% helix, 19% strand	P19388
F	DNA-directed RNA polymerases I, II, and III subunit RPABC2	protein	68	34% helix, 19% strand	P61218
G	DNA-directed RNA polymerase II subunit RPB7	protein	167	6% helix, 44% strand	P62487
H	DNA-directed RNA polymerases I, II, and III subunit RPABC3	protein	146	0% helix, 37% strand	P52434
I	DNA-directed RNA polymerase II subunit RPB9	protein	110	3% helix, 31% strand	P36954
J	DNA-directed RNA polymerases I, II, and III subunit RPABC5	protein	64	30% helix, 0% strand	P62875
K	DNA-directed RNA polymerase II subunit RPB11-a	protein	111	35% helix, 23% strand	P52435
L	DNA-directed RNA polymerases I, II, and III subunit RPABC4	protein	37	0% helix, 24% strand	P53803
M	DNA-directed RNA polymerase II subunit GRINL1A	protein	62	21% helix, 2% strand	P0CAP2

Ligands and binding sites

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

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	1110	0.87	0.88	110	empty
2	1160	0.80	0.82	122	empty
3	1005	0.80	0.82	80	empty
4	646	0.79	0.84	68	empty
5	768	0.78	0.82	84	empty

Interfaces

27 interfaces between chains.

A–B · 3956 Å² buried · 36 hydrogen bonds · protein-protein
A–E · 2348 Å² buried · 21 hydrogen bonds · protein-protein
C–K · 2264 Å² buried · 9 hydrogen bonds · protein-protein
A–H · 2196 Å² buried · 24 hydrogen bonds · protein-protein
A–F · 1953 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

6DRD · RNA Pol II(G) · the same entry in another collection · chain K against K, 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 P24928
Every structure of UniProt P30876
Every structure of UniProt P19387
Every structure of UniProt O15514
Every structure of UniProt P19388
Every structure of UniProt P61218
Every structure of UniProt P62487
Every structure of UniProt P52434
Every structure of UniProt P36954
Every structure of UniProt P62875
Every structure of UniProt P52435
Every structure of UniProt P53803
Every structure of UniProt P0CAP2
Elsewhere: RCSB PDB 6DRD · PDBe 6DRD · UniProt P24928 · UniProt P30876 · UniProt P19387 · UniProt O15514 · UniProt P19388 · UniProt P61218 · UniProt P62487 · UniProt P52434 · UniProt P36954 · UniProt P62875 · UniProt P52435 · UniProt P53803 · UniProt P0CAP2

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