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MolNFT v1 · #138072 · protein + DNA + RNA

2-se-T2/4-DNA and native RNA hybrid in complex with RNase H catalytic domain D132N mutant

5W7N · RNA (5'-R(*UP*CP*GP*AP*CP*A)-3'): “2-se-T2/4-DNA and native RNA hybrid in complex with RNase H catalytic domain D132N mutant”. X-ray diffraction, 1 ligand (MG). MolNFT v1 #138072 on GenesisL1: 3D structure, binding sites and pockets…

PDB
5W7N
Type
protein + DNA + RNA
Length
144 residues
Chains
3
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
RNA (5'-R(*UP*CP*GP*AP*CP*A)-3'); DNA (5'-D(*AP*(US3)P*GP*(US3)P*CP*G)-3'); Ribonuclease H
EC
3.1.26.4
UniProt
Q9KEI9
Ligands
MG

Structure

x-ray diffraction · 3 distinct chains · 34% helix, 24% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
BRNA (5'-R(*UP*CP*GP*AP*CP*A)-3')rna6——
CDNA (5'-D(*AP*(US3)P*GP*(US3)P*CP*G)-3')dna6——
ARibonuclease H (EC 3.1.26.4)protein13234% helix, 24% strandQ9KEI9

Ligands and binding sites

  • MG · Magnesium ion · metal · 2 copies · chains B, A

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

Interfaces

3 interfaces between chains.

  • C–A · 373 Ų buried · 14 hydrogen bonds · protein-nucleic
  • B–C · 267 Ų buried · 17 hydrogen bonds · nucleic-nucleic
  • B–A · 245 Ų buried · 8 hydrogen bonds · protein-nucleic

Modifications

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

Compared structures

  • 5W7N · 2-Se-T2/4-DNA and native RNA hybrid in complex with RNase H catalytic domain D132N mutant · the same entry in another collection · chain B against B, TM-score 1.00
  • Q9KEI9 · AlphaFold monomer V2.0 prediction for ribonuclease H (Q9KEI9) · a predicted model of the same protein · chain A against A, TM-score 1.00

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