Structure of PDB 3wvk Chain D

Receptor sequence

>3wvkD (length=298) Species: 71421 (Haemophilus influenzae Rd KW20)

KSALEKLLSLIENLTNQEFKQATNSLISFIYKLNRNEVIELVRSIGILPE
AIKPSSTQEKLFSKAGDIVLAKAFQLLNLNSKPLEQRGNAGDVIALSKEF
NYGLVADAKSFRLSRTAKNQKDFKVKALSEWREDKDYAVLTAPFFQYPTT
KSQIFKQSLDENVLLFSWEHLAILLQLDLEETNIFSFEQLWNFPKKQSKK
TSVSDAENNFMRDFNKYFMDLFKIDKDTLNQLLQKEINFIEERSLIEKEY
WKKQINIIKNFTREEAIEALLKDINMSSKIETIDSFIKGIKSNDRLYL

3D structure

• PDB: 3wvk Analysis of the HindIII-catalyzed reaction by time-resolved crystallography
• Chain: D
• Resolution: 2.0 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	D	K21 R88	K20 R87
BS02	dna	D	A118 N120 P149 T150 T151 K152 S153 Q154	A117 N119 P148 T149 T150 K151 S152 Q153
BS03	dna	D	F20 K21 S56 T58 K61 E86 K122	F19 K20 S55 T57 K60 E85 K121
BS04	dna	D	K125 W132	K124 W131
BS05	dna	D	L49 E60 S64 D93 D108 S111 F112 R113 R116 T117 A118 D123 K125	L48 E59 S63 D92 D107 S110 F111 R112 R115 T116 A117 D122 K124
BS06	MN	D	D93 D108 A109	D92 D107 A108
BS07	MN	D	Q87 D93	Q86 D92

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:3wvk, PDBe:3wvk, PDBj:3wvk
• PDBsum: 3wvk
• PubMed: 25664735
• UniProt: P43870|T2D3_HAEIN Type II restriction enzyme HindIII (Gene Name=hindIIIR)