Structure of PDB 6dpd Chain A

Receptor sequence

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

EEIIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEF
LAIVHGLRYLKERNSRKPIYSDSQTAIKWVKDKKAKSTLVRNEETALIWK
LVDEAEEWLNTHTYETPILKWQTDKWGEIKADYGRK

3D structure

• PDB: 6dpd Cation trafficking propels RNA hydrolysis.
• Chain: A
• Resolution: 1.46 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 Q134 K180 T183	N45 E49 D72 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 K146 S147 T148	N17 P18 T44 N45 N46 K78 W79 K86 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:6dpd, PDBe:6dpd, PDBj:6dpd
• PDBsum: 6dpd
• PubMed: 30076410
• UniProt: Q9KEI9|RNH1_HALH5 Ribonuclease H (Gene Name=rnhA)