Research workbench

RNA polymerase II complexed with ATP

Analyse RNA polymerase II complexed with ATP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1TWA
Type: protein
Length: 3,485 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA-directed RNA polymerase II largest subunit; DNA-directed RNA polymerase II 140 kda…
EC: 2.7.7.6
UniProt: P04050, P08518, P16370, P20434, P20435, P20436, P27999, P22139, P38902, P40422
Ligands: ATP, ZN, MN
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 10 distinct chains · 32% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-directed RNA polymerase II largest subunit (EC 2.7.7.6)	protein	1352	41% helix, 16% strand	P04050
B	DNA-directed RNA polymerase II 140 kda polypeptide (EC 2.7.7.6)	protein	1091	28% helix, 23% strand	P08518
C	DNA-directed RNA polymerase II 45 kda polypeptide (EC 2.7.7.6)	protein	266	24% helix, 23% strand	P16370
E	DNA-directed RNA polymerases I, II, and III 27 kda polypeptide (EC 2.7.7.6)	protein	215	39% helix, 24% strand	P20434
F	DNA-directed RNA polymerases I, II, and III 23 kda polypeptide (EC 2.7.7.6)	protein	83	33% helix, 16% strand	P20435
H	DNA-directed RNA polymerases I, II, and III 14.5 kda polypeptide (EC 2.7.7.6)	protein	133	0% helix, 41% strand	P20436
I	DNA-directed RNA polymerase II 14.2 kda polypeptide (EC 2.7.7.6)	protein	121	2% helix, 31% strand	P27999
J	DNA-directed RNA polymerases I, II, and III 8.3 kda polypeptide (EC 2.7.7.6)	protein	64	45% helix, 5% strand	P22139
K	DNA-directed RNA polymerase II 13.6 kda polypeptide (EC 2.7.7.6)	protein	114	36% helix, 24% strand	P38902
L	DNA-directed RNA polymerases I, II, and III 7.7 kda polypeptide (EC 2.7.7.6)	protein	46	0% helix, 17% strand	P40422

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · chains A, B
ZN · Zinc ion · metal · 8 copies · chains J, C, I, L, A, B
MN · Manganese (II) ion · metal · 2 copies · chains A, B

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	915	0.88	0.90	109	empty
2	930	0.86	0.87	100	empty
3	823	0.81	0.83	113	empty
4	970	0.79	0.81	86	empty
5	912	0.79	0.81	85	empty

Interfaces

22 interfaces between chains.

A–B · 8513 Å² buried · 117 hydrogen bonds · protein-protein
A–E · 2580 Å² buried · 20 hydrogen bonds · protein-protein
C–K · 2173 Å² buried · 12 hydrogen bonds · protein-protein
A–F · 1990 Å² buried · 19 hydrogen bonds · protein-protein
B–C · 1766 Å² buried · 32 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide (disulfide).

Compared structures

1TWA · RNA polymerase II complexed with ATP · 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 1TWA · PDBe 1TWA · UniProt P04050 · UniProt P08518 · UniProt P16370 · UniProt P20434 · UniProt P20435 · UniProt P20436 · UniProt P27999 · UniProt P22139 · UniProt P38902 · UniProt P40422

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