MolNFT v1 · #46154 · protein

RNA polymerase II form II in 150 mm MN+2

2NVY · DNA-directed RNA polymerase II largest subunit: “RNA polymerase II form II in 150 mm MN+2”. X-ray diffraction, 2 ligands (ZN, MN), 20 pockets (best druggability 0.88). MolNFT v1 #46154 on GenesisL1: 3D structure, binding sites and…

PDB: 2NVY
Type: protein
Length: 3,558 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: ZN, MN
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 10 distinct chains · 32% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-directed RNA polymerase II largest subunit (EC 2.7.7.6)	protein	1419	39% helix, 16% strand	P04050
B	DNA-directed RNA polymerase II 140 kda polypeptide (EC 2.7.7.6)	protein	1094	29% helix, 23% strand	P08518
C	DNA-directed RNA polymerase II 45 kda polypeptide (EC 2.7.7.6)	protein	266	23% helix, 22% strand	P16370
E	DNA-directed RNA polymerases I, II, and III 27 kda polypeptide (EC 2.7.7.6)	protein	215	40% helix, 23% strand	P20434
F	DNA-directed RNA polymerases I, II, and III 23 kda polypeptide (EC 2.7.7.6)	protein	84	31% helix, 17% strand	P20435
H	DNA-directed RNA polymerases I, II, and III 14.5 kda polypeptide (EC 2.7.7.6)	protein	133	2% helix, 35% strand	P20436
I	DNA-directed RNA polymerase II subunit 9 (EC 2.7.7.6)	protein	122	0% helix, 30% strand	P27999
J	DNA-directed RNA polymerases I/II/III subunit 10 (EC 2.7.7.6)	protein	65	43% helix, 5% strand	P22139
K	DNA-directed RNA polymerase II 13.6 kda polypeptide (EC 2.7.7.6)	protein	114	38% 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, 11% strand	P40422

Ligands and binding sites

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	1037	0.88	0.89	145	empty
2	1120	0.85	0.86	107	empty
3	993	0.81	0.82	90	empty
4	500	0.77	0.85	81	empty
5	395	0.76	0.86	47	empty

Interfaces

23 interfaces between chains.

A–B · 9102 Å² buried · 134 hydrogen bonds · protein-protein
A–E · 2641 Å² buried · 27 hydrogen bonds · protein-protein
C–K · 2111 Å² buried · 13 hydrogen bonds · protein-protein
A–F · 2050 Å² buried · 24 hydrogen bonds · protein-protein
B–C · 1801 Å² buried · 35 hydrogen bonds · protein-protein

Compared structures

2NVY · RNA Polymerase II form II in 150 mM Mn+2 · 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 2NVY · PDBe 2NVY · UniProt P04050 · UniProt P08518 · UniProt P16370 · UniProt P20434 · UniProt P20435 · UniProt P20436 · UniProt P27999 · UniProt P22139 · UniProt P38902 · UniProt P40422

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