Structure of PDB 3wvp Chain B

Receptor sequence

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

KSALEKLLSLIENLTNQEFKQATNSLISFIYKLNRNEVIELVRSIGILPE
AIKPSSTQEKLFSKAGDIVLAKAFQLLNLNSKPLEQRGNAGDVIALSKEF
NYGLVADAKSFRLSRTAKNQKDFKVKALSEWREDKDYAVLTAPFFQYPTT
KSQIFKQSLDENVLLFSWEHLAILLQLDLEETNIFSFEQLWNFPKKQSKK
TSVSDAENNFMRDFNKYFMDLFKIDKDTLNQLLQKEINFIEERSLIEKEY
WKKQINIIKNFTREEAIEALLKDINMSSKIETIDSFIKGIKSNDRLYL

3D structure

• PDB: 3wvp Analysis of the HindIII-catalyzed reaction by time-resolved crystallography
• Chain: B
• Resolution: 2.3 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	B	L49 E60 S64 R88 N90 D93 D108 S111 F112 R113 R116 T117 A118 D123 K125 W132	L48 E59 S63 R87 N89 D92 D107 S110 F111 R112 R115 T116 A117 D122 K124 W131
BS02	dna	B	F20 K21 S56 T58 K61 E86 R88 N120 Q121 K122 P149 T150 T151 K152 S153 Q154	F19 K20 S55 T57 K60 E85 R87 N119 Q120 K121 P148 T149 T150 K151 S152 Q153
BS03	dna	B	F20 K21 S56 T58 K61 E86 R88 K122	F19 K20 S55 T57 K60 E85 R87 K121
BS04	dna	B	L49 E60 S64 D93 D108 S111 F112 R113 R116 T117 A118 D123	L48 E59 S63 D92 D107 S110 F111 R112 R115 T116 A117 D122
BS05	dna	B	R88 G89 N90 K125 W132	R87 G88 N89 K124 W131
BS06	dna	B	A118 N120 P149 T150 T151 K152 S153 Q154	A117 N119 P148 T149 T150 K151 S152 Q153
BS07	MN	B	D93 D108 A109	D92 D107 A108

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