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Crystal structure of 10 subunit RNA polymerase II in complex with the inhibitor alpha-amanitin

Analyse Crystal structure of 10 subunit RNA polymerase II in complex with the inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3CQZ
Type: protein
Length: 3,438 residues
Chains: 11
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, P85421
Ligands: ZN
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 11 distinct chains · 31% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA-directed RNA polymerase II subunit RPB1 (EC 2.7.7.6)	protein	1349	39% helix, 17% strand	P04050
B	DNA-directed RNA polymerase II subunit RPB2 (EC 2.7.7.6)	protein	1061	29% helix, 24% strand	P08518
C	DNA-directed RNA polymerase II subunit RPB3	protein	265	25% helix, 26% strand	P16370
E	DNA-directed RNA polymerases I, II, and III subunit RPABC1	protein	213	36% helix, 23% strand	P20434
F	DNA-directed RNA polymerases I, II, and III subunit RPABC2	protein	84	30% helix, 15% strand	P20435
H	DNA-directed RNA polymerases I, II, and III subunit RPABC3	protein	116	0% helix, 46% strand	P20436
I	DNA-directed RNA polymerase II subunit RPB9	protein	121	2% helix, 31% strand	P27999
J	DNA-directed RNA polymerases I, II, and III subunit RPABC5	protein	65	43% helix, 5% strand	P22139
K	DNA-directed RNA polymerase II subunit RPB11	protein	113	38% helix, 23% strand	P38902
L	DNA-directed RNA polymerases I, II, and III subunit RPABC4	protein	43	0% helix, 23% strand	P40422
M	Alpha-amanitin	protein	8	0% helix, 25% strand	P85421

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	952	0.88	0.90	117	empty
2	718	0.86	0.90	76	empty
3	652	0.78	0.83	64	empty
4	338	0.76	0.87	61	empty
5	1183	0.76	0.79	90	empty

Interfaces

24 interfaces between chains.

A–B · 7921 Å² buried · 103 hydrogen bonds · protein-protein
A–E · 2462 Å² buried · 26 hydrogen bonds · protein-protein
C–K · 2052 Å² buried · 14 hydrogen bonds · protein-protein
A–F · 1989 Å² buried · 17 hydrogen bonds · protein-protein
B–C · 1828 Å² buried · 34 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (nonstandard, hydroxylation, oxidation).

Compared structures

3CQZ · Crystal structure of 10 subunit RNA polymerase II in complex with the inhibitor… · the same entry in another collection · chain H against H, TM-score 1.00
P85421 · AlphaFold monomer V2.0 prediction for alpha-amanitin proprotein (P85421) · a predicted model of the same protein · chain M against A, TM-score 0.34

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
Every structure of UniProt P85421
Elsewhere: RCSB PDB 3CQZ · PDBe 3CQZ · UniProt P04050 · UniProt P08518 · UniProt P16370 · UniProt P20434 · UniProt P20435 · UniProt P20436 · UniProt P27999 · UniProt P22139 · UniProt P38902 · UniProt P40422 · UniProt P85421

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