Research workbench

Pol II elongation complex with an N6-methyladenine-containing template

Analyse Pol II elongation complex with an N6-methyladenine-containing template in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5W4U
Type: protein + DNA + RNA
Length: 3,543 residues
Chains: 13
Method: x-ray diffraction
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
UniProt: P04050, P08518, P16370, P20434, P20435, P20436, P27999, P22139, P38902, P40422
Ligands: ZN, MG
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 13 distinct chains · 31% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-directed RNA polymerase II subunit RPB1 (EC 2.7.7.6)	protein	1371	39% helix, 14% strand	P04050
B	DNA-directed RNA polymerase II subunit RPB2 (EC 2.7.7.6)	protein	1089	28% helix, 24% strand	P08518
C	DNA-directed RNA polymerase II subunit RPB3	protein	266	21% helix, 26% strand	P16370
E	DNA-directed RNA polymerases I, II, and III subunit RPABC1	protein	213	38% helix, 23% strand	P20434
F	DNA-directed RNA polymerases I, II, and III subunit RPABC2	protein	84	31% helix, 15% strand	P20435
H	DNA-directed RNA polymerases I, II, and III subunit RPABC3	protein	130	0% helix, 52% strand	P20436
I	DNA-directed RNA polymerase II subunit RPB9	protein	115	4% helix, 27% strand	P27999
J	DNA-directed RNA polymerases I, II, and III subunit RPABC5	protein	65	45% helix, 5% strand	P22139
K	DNA-directed RNA polymerase II subunit RPB11	protein	114	37% helix, 24% strand	P38902
L	DNA-directed RNA polymerases I, II, and III subunit RPABC4	protein	44	0% helix, 25% strand	P40422
T	29MER template DNA	dna	29	—	—
N	14MER non-template DNA	dna	14	—	—
R	9MER RNA	rna	9	—	—

Ligands and binding sites

ZN · Zinc ion · metal · 8 copies · chains A, B, C, I, J, L
MG · Magnesium ion · metal · chains A, 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	951	0.88	0.90	123	empty
2	956	0.85	0.87	109	empty
3	906	0.83	0.85	76	empty
4	582	0.78	0.84	60	empty
5	748	0.77	0.82	82	empty

Interfaces

30 interfaces between chains.

A–B · 9623 Å² buried · 131 hydrogen bonds · protein-protein
A–E · 2243 Å² buried · 26 hydrogen bonds · protein-protein
C–K · 2097 Å² buried · 12 hydrogen bonds · protein-protein
A–F · 1996 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 1855 Å² buried · 30 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 modified (nucleotide modification).

Compared structures

5W4U · Pol II elongation complex with an N6-methyladenine-containing template · the same entry in another collection · chain A against A, 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 P04050
Every structure of UniProt P08518
Every structure of UniProt P16370
Every structure of UniProt P20434
Every structure of UniProt P20435
Every structure of UniProt P20436
Every structure of UniProt P27999
Every structure of UniProt P22139
Every structure of UniProt P38902
Every structure of UniProt P40422
Elsewhere: RCSB PDB 5W4U · PDBe 5W4U · UniProt P04050 · UniProt P08518 · UniProt P16370 · UniProt P20434 · UniProt P20435 · UniProt P20436 · UniProt P27999 · UniProt P22139 · UniProt P38902 · UniProt P40422

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.