MolNFT v1 · #63795 · protein

12-subunit RNA polymerase II refined with zn-sad data

3FKI · DNA-directed RNA polymerase II subunit RPB1: “12-subunit RNA polymerase II refined with zn-sad data”. X-ray diffraction, 2 ligands (ZN, MG), 20 pockets (best druggability 0.85). MolNFT v1 #63795 on GenesisL1: 3D structure, binding…

PDB: 3FKI
Type: protein
Length: 3,952 residues
Chains: 12
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, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422
Ligands: ZN, MG
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 12 distinct chains · 29% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-directed RNA polymerase II subunit RPB1 (EC 2.7.7.6)	protein	1427	37% helix, 15% strand	P04050
B	DNA-directed RNA polymerase II subunit RPB2 (EC 2.7.7.6)	protein	1125	25% helix, 22% strand	P08518
C	DNA-directed RNA polymerase II subunit RPB3	protein	267	25% helix, 24% strand	P16370
D	DNA-directed RNA polymerase II subunit RPB4	protein	178	46% helix, 5% strand	P20433
E	DNA-directed RNA polymerases I, II, and III subunit RPABC1	protein	214	38% helix, 23% strand	P20434
F	DNA-directed RNA polymerases I, II, and III subunit RPABC2	protein	87	30% helix, 15% strand	P20435
G	DNA-directed RNA polymerase II subunit RPB7	protein	171	11% helix, 48% strand	P34087
H	DNA-directed RNA polymerases I, II, and III subunit RPABC3	protein	136	0% helix, 40% strand	P20436
I	DNA-directed RNA polymerase II subunit RPB9	protein	119	0% helix, 25% strand	P27999
J	DNA-directed RNA polymerases I, II, and III subunit RPABC5	protein	66	38% helix, 2% strand	P22139
K	DNA-directed RNA polymerase II subunit RPB11	protein	115	38% helix, 24% strand	P38902
L	DNA-directed RNA polymerases I, II, and III subunit RPABC4	protein	47	0% helix, 15% strand	P40422

Ligands and binding sites

ZN · Zinc ion · metal · 8 copies · chains A, B, C, I, J, L
MG · Magnesium ion · metal · chains A

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	853	0.85	0.87	106	empty
2	895	0.84	0.86	118	empty
3	1010	0.84	0.85	105	empty
4	156	0.78	0.95	29	empty
5	1010	0.78	0.80	96	empty

Interfaces

29 interfaces between chains.

A–B · 10103 Å² buried · 145 hydrogen bonds · protein-protein
D–G · 2517 Å² buried · 21 hydrogen bonds · protein-protein
A–F · 2292 Å² buried · 15 hydrogen bonds · protein-protein
A–E · 2251 Å² buried · 24 hydrogen bonds · protein-protein
C–K · 2198 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

3FKI · 12-Subunit RNA Polymerase II Refined with Zn-SAD data · the same entry in another collection · chain L against L, 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 P20433
Every structure of UniProt P20434
Every structure of UniProt P20435
Every structure of UniProt P34087
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 3FKI · PDBe 3FKI · UniProt P04050 · UniProt P08518 · UniProt P16370 · UniProt P20433 · UniProt P20434 · UniProt P20435 · UniProt P34087 · UniProt P20436 · UniProt P27999 · UniProt P22139 · UniProt P38902 · UniProt P40422

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