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MolNFT v1 · #104225 · protein + DNA

Polymerase-damaged DNA complex

4Q43 · DNA polymerase IV: “Polymerase-damaged DNA complex”. X-ray diffraction, 2 ligands (0KX, MG), 7 pockets (best druggability 0.82). MolNFT v1 #104225 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB
4Q43
Type
protein + DNA
Length
751 residues
Chains
6
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
DNA polymerase IV; DNA (5'-D(*TP*CP*TP*(RDG) P*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3…
EC
2.7.7.7
UniProt
Q47155
Ligands
0KX, MG
Pockets
7 · best druggability 0.82

Structure

x-ray diffraction · 4 distinct chains · 37% helix, 22% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
A, FDNA polymerase IV (EC 2.7.7.7)protein34237% helix, 22% strandQ47155
B, GDNA (5'-D(*TP*CP*TP*(RDG) P*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')dna18——
CDNA (5'- D(*T*CP*TP*AP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')dna17——
HDNA (5'- D(*T*CP*TP*AP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')dna14——

Ligands and binding sites

  • 0KX · 2'-deoxy-5'-O-[(R)-hydroxy{[(r)-hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]cytidine · ligand · 2 copies · chains A, B, C, F, G, H
  • MG · Magnesium ion · metal · 4 copies · chains A, C, F, H

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

Pockets

7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
19910.820.84730KX, MG
29750.810.82680KX, MG
35790.760.8347empty
44930.750.8444empty
5510.370.8114empty

Interfaces

9 interfaces between chains.

  • A–B · 1115 Ų buried · 28 hydrogen bonds · protein-nucleic
  • F–G · 1082 Ų buried · 23 hydrogen bonds · protein-nucleic
  • B–C · 667 Ų buried · 82 hydrogen bonds · nucleic-nucleic
  • G–H · 641 Ų buried · 74 hydrogen bonds · nucleic-nucleic
  • F–H · 598 Ų buried · 21 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 2 modified (nucleotide modification).

Compared structures

  • 4Q43 · Polymerase-damaged DNA complex · the same entry in another collection · chain H against H, TM-score 1.00
  • Q47155 · AlphaFold monomer V2.0 prediction for DNA polymerase IV (Q47155) · a predicted model of the same protein · chain F against A, TM-score 0.99

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