Structure of PDB 3a4k Chain A

Receptor sequence

>3a4kA (length=297) Species: 71421 (Haemophilus influenzae Rd KW20)

KSALEKLLSLIENLTNQEFKQATNSLISFIYKLNRNEVIELVRSIGILPE
AIKPSSTQEKLFSKAGDIVLAKAFQLLNLNSKPLEQGNAGDVIALSKEFN
YGLVADAKSFRLSRTAKNQKDFKVKALSEWREDKDYAVLTAPFFQYPTTK
SQIFKQSLDENVLLFSWEHLAILLQLDLEETNIFSFEQLWNFPKKQSKKT
SVSDAENNFMRDFNKYFMDLFKIDKDTLNQLLQKEINFIEERSLIEKEYW
KKQINIIKNFTREEAIEALLKDINMSSKIETIDSFIKGIKSNDRLYL

3D structure

• PDB: 3a4k Structures of restriction endonuclease HindIII in complex with its cognate DNA and divalent cations
• Chain: A
• Resolution: 2.17 Å

Enzymatic activity

• Enzyme Commision number: 3.1.21.4: type II site-specific deoxyribonuclease.

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	dna	A	G89 N90 K125 W132	G87 N88 K123 W130
BS02	dna	A	L49 E60 S64 D93 D108 K110 S111 F112 R113 R116 T117 A118 D123 K125	L48 E59 S63 D91 D106 K108 S109 F110 R111 R114 T115 A116 D121 K123
BS03	dna	A	A118 N120 P149 T150 T151 K152 S153 Q154	A116 N118 P147 T148 T149 K150 S151 Q152
BS04	dna	A	F20 S56 T58 K61 K122 N276	F19 S55 T57 K60 K120 N274
BS05	dna	A	K21 Q22 N25 I28	K20 Q21 N24 I27
BS06	dna	A	Y32 K33	Y31 K32
BS07	MN	A	D93 D108 A109	D91 D106 A107

Gene Ontology

Molecular Function

• GO:0004519 endonuclease activity
• GO:0009036 type II site-specific deoxyribonuclease activity

Biological Process

• GO:0009307 DNA restriction-modification system

External links

• PDB: RCSB:3a4k, PDBe:3a4k, PDBj:3a4k
• PDBsum: 3a4k
• PubMed: 19966419
• UniProt: P43870|T2D3_HAEIN Type II restriction enzyme HindIII (Gene Name=hindIIIR)