Structure of PDB 6dpf Chain A

Receptor sequence

>6dpfA (length=136) Species: 272558 (Halalkalibacterium halodurans C-125)

EEIIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEF
LAIVHGLRYLKERNSRKPIYSDSQTAIKWVKDKKAKSTLVRNEETALIWK
LVDEAEEWLNTHTYETPILKWQTDKWGEIKADYGRK

3D structure

• PDB: 6dpf Cation trafficking propels RNA hydrolysis.
• Chain: A
• Resolution: 1.56 Å

Enzymatic activity

• Enzyme Commision number: 3.1.26.4: ribonuclease H.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	rna	A	N105 E109 D132 S133 Q134 K180 T183	N45 E49 D72 S73 Q74 K120 T123
BS02	rna	A	D71 V72 G73 S74 G76 N105 D132 R195 K196	D11 V12 G13 S14 G16 N45 D72 R135 K136
BS03	dna	A	N77 P78 T104 N105 N106 K138 W139 S147 T148	N17 P18 T44 N45 N46 K78 W79 S87 T88
BS04	MN	A	D71 D192	D11 D132
BS05	MN	A	D71 E109 D132	D11 E49 D72
BS06	MN	A	D163 E166	D103 E106

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0004523 RNA-DNA hybrid ribonuclease activity

External links

• PDB: RCSB:6dpf, PDBe:6dpf, PDBj:6dpf
• PDBsum: 6dpf
• PubMed: 30076410
• UniProt: Q9KEI9|RNH1_HALH5 Ribonuclease H (Gene Name=rnhA)