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MolNFT v1 · #90048 · protein + DNA

Pfv intasome freeze-trapped prior to 3'-processing, mn-bound form (ui- mn)

4E7I · Pro-pol polyprotein: “Pfv intasome freeze-trapped prior to 3'-processing, mn-bound form (ui- mn)”. X-ray diffraction, 3 ligands (MN, ZN, SO4), 11 pockets (best druggability 0.70). MolNFT v1 #90048 on GenesisL1: 3D structure, binding…

PDB
4E7I
Type
protein + DNA
Length
590 residues
Chains
4
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Pro-pol polyprotein; DNA (5'- D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*CP*A)…
EC
2.7.7.49, 2.7.7.7, 3.1.26.4, 3.4.23.-
UniProt
P14350
Ligands
MN, ZN, SO4
Pockets
11 · best druggability 0.70

Structure

x-ray diffraction · 4 distinct chains · 35% helix, 20% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
APro-pol polyprotein (EC 2.7.7.49, 2.7.7.7, 3.1.26.4, 3.4.23.-)protein36834% helix, 21% strandP14350
BPro-pol polyprotein (EC 2.7.7.49, 2.7.7.7, 3.1.26.4, 3.4.23.-)protein18439% helix, 16% strandP14350
CDNA (5'- D(*AP*TP*TP*GP*TP*CP*AP*TP*GP*GP*AP*AP*TP*TP*TP*CP*GP*CP*A)-3')dna19——
DDNA (5'- D(*TP*GP*CP*GP*AP*AP*AP*TP*TP*CP*CP*AP*TP*GP*AP*CP*AP*AP*T)-3')dna19——

Ligands and binding sites

  • MN · Manganese (II) ion · metal · 3 copies · chains A, D, B
  • ZN · Zinc ion · metal · chains A
  • SO4 · Sulfate ion · ion · 4 copies · chains A, C, B
  • GOL · Glycerol · additive · 9 copies · chains A, C, B, D
  • MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A, D
  • HEZ · Hexane-1,6-diol · additive · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
15910.700.7842SO4, HEZ
23710.670.8153SO4, GOL
3620.580.9021empty
4700.490.8415empty
5980.440.7914empty

Interfaces

4 interfaces between chains.

  • A–B · 1429 Ų buried · 18 hydrogen bonds · protein-protein
  • A–C · 1150 Ų buried · 24 hydrogen bonds · protein-nucleic
  • C–D · 739 Ų buried · 66 hydrogen bonds · nucleic-nucleic
  • A–D · 665 Ų buried · 10 hydrogen bonds · protein-nucleic

Compared structures

  • 4E7I · PFV intasome freeze-trapped prior to 3'-processing, Mn-bound form (UI-Mn) · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

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