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RNA polymerase-GFH1 complex (crystal type 2)

Analyse RNA polymerase-GFH1 complex (crystal type 2) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
3AOI
Type
protein + DNA + RNA
Length
9,270 residues
Chains
24
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA-directed RNA polymerase subunit alpha; DNA-directed RNA polymerase subunit beta…
EC
2.7.7.6
UniProt
Q5SHR6, Q8RQE9, Q8RQE8, Q8RQE7, Q5SJG6
Ligands
ZN, MG
Pockets
20 · best druggability 0.89

Structure

x-ray diffraction · 17 distinct chains · 33% helix, 20% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
A, B, F, LDNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)protein22322% helix, 36% strandQ5SHR6
CDNA-directed RNA polymerase subunit beta (EC 2.7.7.6)protein108327% helix, 24% strandQ8RQE9
DDNA-directed RNA polymerase subunit beta' (EC 2.7.7.6)protein131638% helix, 14% strandQ8RQE8
E, J, ODNA-directed RNA polymerase subunit omega (EC 2.7.7.6)protein9351% helix, 4% strandQ8RQE7
GDNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)protein22422% helix, 39% strandQ5SHR6
HDNA-directed RNA polymerase subunit beta (EC 2.7.7.6)protein108026% helix, 24% strandQ8RQE9
IDNA-directed RNA polymerase subunit beta' (EC 2.7.7.6)protein126240% helix, 14% strandQ8RQE8
KDNA-directed RNA polymerase subunit alpha (EC 2.7.7.6)protein22521% helix, 37% strandQ5SHR6
MDNA-directed RNA polymerase subunit beta (EC 2.7.7.6)protein108426% helix, 23% strandQ8RQE9
NDNA-directed RNA polymerase subunit beta' (EC 2.7.7.6)protein132738% helix, 15% strandQ8RQE8
PDNA (5'- D(*GP*GP*TP*CP*TP*GP*TP*AP*TP*CP*AP*CP*GP*AP*GP*CP*CP*A*CP*CP*GP*CP*C P*GP*CP*AP*T)-3')dna7——
Q, URNA (5'- R(*CP*CP*CP*GP*GP*AP*AP*GP*AP*UP*CP*AP*UP*CP*UP*UP*CP*CP*GP*GP*GP*GP* GP*AP*U*GP*CP*GP*GP*CP*GP*G)-3')rna7——
RDNA (5'- D(*GP*GP*TP*CP*TP*GP*TP*AP*TP*CP*AP*CP*GP*AP*GP*CP*CP*A*CP*CP*GP*CP*C P*GP*CP*AP*T)-3')dna6——
SRNA (5'- R(*CP*CP*CP*GP*GP*AP*AP*GP*AP*UP*CP*AP*UP*CP*UP*UP*CP*CP*GP*GP*GP*GP* GP*AP*U*GP*CP*GP*GP*CP*GP*G)-3')rna8——
TDNA (5'- D(*GP*GP*TP*CP*TP*GP*TP*AP*TP*CP*AP*CP*GP*AP*GP*CP*CP*A*CP*CP*GP*CP*C P*GP*CP*AP*T)-3')dna5——
XAnti-cleavage anti-grea transcription factor GFH1protein15440% helix, 21% strandQ5SJG6
Y, ZAnti-cleavage anti-grea transcription factor GFH1protein15241% helix, 20% strandQ5SJG6

Ligands and binding sites

  • ZN · Zinc ion · metal · 3 copies · chains N, D, I
  • MG · Magnesium ion · metal · 3 copies · chains D, Q, I, S, N, U, Z

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
110130.890.91125MG
210580.880.90120MG
311170.870.88108empty
47420.860.9094empty
56950.860.8989empty

Interfaces

56 interfaces between chains.

  • H–I · 8383 Ų buried · 94 hydrogen bonds · protein-protein
  • M–N · 8371 Ų buried · 100 hydrogen bonds · protein-protein
  • C–D · 8220 Ų buried · 96 hydrogen bonds · protein-protein
  • N–O · 2452 Ų buried · 27 hydrogen bonds · protein-protein
  • I–J · 2450 Ų buried · 29 hydrogen bonds · protein-protein

Compared structures

  • 3AOI · RNA polymerase-Gfh1 complex (Crystal type 2) · the same entry in another collection · chain K against K, TM-score 1.00

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