Structure of PDB 5fbd Chain A

Receptor sequence

>5fbdA (length=267) Species: 510516 (Aspergillus oryzae RIB40)

WGNLGHETVAYIAQSFVASSTESFCQNILGDDSTSYLANVATWADTYKYT
DAGEFSKPYHFIDAQDNPPQSCGVDYDRDCGSAGCSISAIQNYTNILLES
PNGSEALNALKFVVHIIGDIHQPLHDENLEAGGNGIDVTYDGETTNLHHI
WDTNMPEEAAGGYSLSVAKTYADLLTERIKTGTYSSKKDSWTDGIDIKDP
VSTSMIWAADANTYVCSTVLDDGLAYINSTDLSGEYYDKSQPVFEELIAK
AGYRLAAWLDLIASQPS

3D structure

• PDB: 5fbd Structural and Catalytic Properties of S1 Nuclease from Aspergillus oryzae Responsible for Substrate Recognition, Cleavage, Non-Specificity, and Inhibition.
• Chain: A
• Resolution: 1.75 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): W21 H26 D65 K68 H80 H135 D139 H145 H168 D172
• Catalytic site (residue number reindexed from 1): W1 H6 D45 K48 H60 H115 D119 H125 H148 D152
• Enzyme Commision number: 3.1.30.1: Aspergillus nuclease S1.

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	ZN	A	W21 H26 D139	W1 H6 D119
BS02	ZN	A	D65 H80 H135 D139	D45 H60 H115 D119
BS03	ZN	A	H145 H168 D172	H125 H148 D152
BS04	PO4	A	W21 D65 K68 H80 D139 H145 D172	W1 D45 K48 H60 D119 H125 D152
BS05	DCZ	A	K68 F81 D83 H145 A151 N154 H168	K48 F61 D63 H125 A131 N134 H148

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0004518 nuclease activity
• GO:0004519 endonuclease activity
• GO:0016788 hydrolase activity, acting on ester bonds
• GO:0046872 metal ion binding

Biological Process

• GO:0006308 DNA catabolic process

Cellular Component

• GO:0005575 cellular_component

External links

• PDB: RCSB:5fbd, PDBe:5fbd, PDBj:5fbd
• PDBsum: 5fbd
• PubMed: 28036383
• UniProt: P24021|NUS1_ASPOR Nuclease S1 (Gene Name=nucS)