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Crystal structure of yeast RNA polymerase II encountering oxidative cyclopurine DNA lesions

Analyse Crystal structure of yeast RNA polymerase II encountering oxidative cyclopurine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4X6A
Type: protein + DNA + RNA
Length: 3,560 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, P20434, P20435, P20436, P27999, P22139, P38902, P40422
Ligands: ZN
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 12 distinct chains · 29% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-directed RNA polymerase II subunit RPB1 (EC 2.7.7.6)	protein	1395	37% helix, 14% strand	P04050
B	DNA-directed RNA polymerase II subunit RPB2 (EC 2.7.7.6)	protein	1104	26% helix, 22% strand	P08518
C	DNA-directed RNA polymerase II subunit RPB3	protein	266	22% helix, 26% strand	P16370
E	DNA-directed RNA polymerases I, II, and III subunit RPABC1	protein	214	39% helix, 19% strand	P20434
F	DNA-directed RNA polymerases I, II, and III subunit RPABC2	protein	84	29% helix, 17% strand	P20435
H	DNA-directed RNA polymerases I, II, and III subunit RPABC3	protein	133	0% helix, 46% strand	P20436
I	DNA-directed RNA polymerase II subunit RPB9	protein	119	3% helix, 29% strand	P27999
J	DNA-directed RNA polymerases I, II, and III subunit RPABC5	protein	65	43% helix, 0% strand	P22139
K	DNA-directed RNA polymerase II subunit RPB11	protein	114	38% helix, 20% strand	P38902
L	DNA-directed RNA polymerases I, II, and III subunit RPABC4	protein	46	0% helix, 15% strand	P40422
R	RNA_9 mer	rna	9	—	—
T	Template DNA _29 mer	dna	11	—	—

Ligands and binding sites

ZN · Zinc ion · metal · 8 copies · chains A, B, 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	575	0.86	0.92	75	empty
2	363	0.84	0.93	56	empty
3	954	0.81	0.83	71	empty
4	650	0.80	0.85	62	empty
5	1006	0.80	0.82	92	empty

Interfaces

26 interfaces between chains.

A–B · 10030 Å² buried · 119 hydrogen bonds · protein-protein
A–E · 2228 Å² buried · 28 hydrogen bonds · protein-protein
C–K · 2155 Å² buried · 14 hydrogen bonds · protein-protein
A–F · 1839 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 1806 Å² buried · 31 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide, 1 modified (disulfide, nucleotide modification).

Compared structures

4X6A · Crystal structure of yeast RNA polymerase II encountering oxidative Cyclopurine DNA… · 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 4X6A · PDBe 4X6A · UniProt P04050 · UniProt P08518 · UniProt P16370 · UniProt P20434 · UniProt P20435 · UniProt P20436 · UniProt P27999 · UniProt P22139 · UniProt P38902 · UniProt P40422

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