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Alpha-amanitin inhibited complete RNA polymerase II elongation complex

Analyse Alpha-amanitin inhibited complete RNA polymerase II elongation complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
2VUM
Type
protein + DNA + RNA
Length
3,969 residues
Chains
16
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, P85421
Ligands
ZN, MG
Pockets
20 · best druggability 0.87

Structure

x-ray diffraction · 16 distinct chains · 29% helix, 18% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ADNA-directed RNA polymerase II subunit RPB1 (EC 2.7.7.6)protein141838% helix, 14% strandP04050
BDNA-directed RNA polymerase II subunit RPB2 (EC 2.7.7.6)protein110627% helix, 21% strandP08518
CDNA-directed RNA polymerase II subunit RPB3 (EC 2.7.7.6)protein26623% helix, 17% strandP16370
DDNA-directed RNA polymerase II subunit RPB4 (EC 2.7.7.6)protein17743% helix, 6% strandP20433
EDNA-directed RNA polymerases I, II, and III subunit RPABC1 (EC 2.7.7.6)protein21432% helix, 19% strandP20434
FDNA-directed RNA polymerases I, II, and III subunit RPABC2 (EC 2.7.7.6)protein8431% helix, 14% strandP20435
GDNA-directed RNA polymerase II subunit RPB7 (EC 2.7.7.6)protein1719% helix, 44% strandP34087
HDNA-directed RNA polymerases I, II, and III subunit RPABC3 (EC 2.7.7.6)protein1332% helix, 41% strandP20436
IDNA-directed RNA polymerase II subunit RPB9 (EC 2.7.7.6)protein1193% helix, 22% strandP27999
JDNA-directed RNA polymerases I, II, and III subunit RPABC5 (EC 2.7.7.6)protein6546% helix, 0% strandP22139
KDNA-directed RNA polymerase II subunit RPB11 (EC 2.7.7.6)protein11432% helix, 24% strandP38902
LDNA-directed RNA polymerases I, II, and III subunit RPABC4protein460% helix, 9% strandP40422
MAmatoxinprotein80% helix, 0% strandP85421
N5'-D(*AP*AP*AP*CP*TP*AP*CP*TP*TP*GP *AP*GP*CP*T)-3'dna13——
P5'-R(*AP*AP*AP*GP*AP*CP*CP*AP*GP*GP*C)-3'rna10——
T5'-D(*AP*GP*CP*TP*CP*AP*AP*GP*TP*AP *GP*TP*TP*AP*CP*GP*CP*CP*BRUP*GP*GP*TP*CP*AP*TP*T)-3'dna25——

Ligands and binding sites

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

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.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
111630.870.88129empty
26910.860.9081empty
311610.810.8386empty
47980.810.8491empty
56900.810.8568empty

Interfaces

38 interfaces between chains.

  • A–B · 9825 Ų buried · 126 hydrogen bonds · protein-protein
  • D–G · 2291 Ų buried · 19 hydrogen bonds · protein-protein
  • A–E · 2250 Ų buried · 25 hydrogen bonds · protein-protein
  • A–F · 2164 Ų buried · 16 hydrogen bonds · protein-protein
  • C–K · 2155 Ų buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 modified (nonstandard, hydroxylation, nucleotide modification, oxidation).

Compared structures

  • 2VUM · Alpha-amanitin inhibited complete RNA polymerase II elongation complex · the same entry in another collection · chain T against T, TM-score 1.00

Analyse

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