Structure of PDB 5ld2 Chain B

Receptor sequence
>5ld2B (length=1151) Species: 83333 (Escherichia coli K-12) [Search protein sequence]
AETLDPLRLPLQGERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPL
TVEELLVVTFTEAATAELRGRIRSNIHELRIACLRETTDNPLYERLLEEI
DDKAQAAQWLLLAERQMDEAAVFTIHGFCQRMLNLNAFESGMLFEQQLIE
DESLLRYQACADFWRRHCYPLPREIAQVVFETWKGPQALLRDINRYLQGE
APVIKAPPPDDETLASRHAQIVARIDTVKQQWRDAVGELDALIESSGIDR
RKFNRSNQAKWIDKISAWAEEETNSYQLPESLEKFTPRHPLFEAIDQLLA
EPLSIRDLVITRALAEIRETVAREKRRRGELGFDDMLSRLDSALRSESGE
VLAAAIRTRFPVAMIDEFQDTDPQQYRIFRRIWHHQPETALLLIGDPKQA
IYAFRGADIFTYMKARSEVHAHYTLDTNWRSAPGMVNSVNKLFSQTDDAF
MFREIPFIPVKSAGKNQALRFVFKGETQPAMKMWLMEGESCGVGDYQSTM
AQVCAAQIRDWLQAGQRGEALLMNGDDARPVRASDISVLVRSRQEAAQVR
DALTLLEIPSVYLSNRDSVFETLEAQEMLWLLQAVMTPERENTLRSALAT
SMMGLNALDIETLNNDEHAWDVVVEEFDGYRQIWRKRGVMPMLRALMSAR
NIAENLLATAGGERRLTDILHISELLQEAGTQLESEHALVRWLSQHILEP
DSNASSQQMRLESDKHLVQIVTIHKSKGLEYPLVWLPFITNFRVQEQAFY
HDRHSFEAVLDLNAAPESVDLAEAERLAEDLRLLYVALTRSVWHCSLGVA
PLVRRRGDKKGDTDVHQSALGRLLQKGEPQDAAGLRTCIEALCDDDIAWQ
TAQTGDNQPWQVNDVSTAELNAKTLQRLPGDNWRVTSYSGLQQRGAGAAA
AAAAAAAAAAAGAAPTLTPHQFPRGASPGTFLHSLFEDLDFTQPVDPNWV
REKLELGGFESQWEPVLTEWITAVLQAPLNETGVSLSQLSARNKQVEMEF
YLPISEPLIASQLDTLIRQFDPLSAGCPPLEFMQVRGMLKGFIDLVFRHE
GRYYLLAYKSNWLGEDSSAYTQQAMAAAMQAHRYDLQYQLYTLALHRYLR
HRIADYDYEHHFGGVIYLFLRGVDKEHPQQGIYTTRPNAGLIALMDEMFA
G
3D structure
PDB5ld2 Mechanism for nuclease regulation in RecBCD.
ChainB
Resolution3.83 Å
3D
structure
Catalytic site residues are labeled in the structure
[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]
Enzymatic activity
Catalytic site (original residue number in PDB) T30
Catalytic site (residue number reindexed from 1) T26
Enzyme Commision number 3.1.11.5: exodeoxyribonuclease V.
5.6.2.4: DNA 3'-5' helicase.
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 S249 S250 I252 R254 Y280 F422 R423 R559 S560 R561 T740 H742 K743 R761 R824 G825 S245 S246 I248 R250 Y276 F404 R405 R541 S542 R543 T722 H724 K725 R743 R806 G807
BS02 ANP B G26 G28 K29 T30 F31 Q417 W447 R448 R808 G22 G24 K25 T26 F27 Q399 W429 R430 R790
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003677 DNA binding
GO:0003678 DNA helicase activity
GO:0004386 helicase activity
GO:0004520 DNA endonuclease activity
GO:0004527 exonuclease activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008094 ATP-dependent activity, acting on DNA
GO:0008854 exodeoxyribonuclease V activity
GO:0015616 DNA translocase activity
GO:0016787 hydrolase activity
GO:0016853 isomerase activity
GO:0016887 ATP hydrolysis activity
GO:0043138 3'-5' DNA helicase activity
GO:0046872 metal ion binding
Biological Process
GO:0000724 double-strand break repair via homologous recombination
GO:0000725 recombinational repair
GO:0006281 DNA repair
GO:0006310 DNA recombination
GO:0009314 response to radiation
GO:0032508 DNA duplex unwinding
GO:0044355 clearance of foreign intracellular DNA
Cellular Component
GO:0005829 cytosol
GO:0009338 exodeoxyribonuclease V complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5ld2, PDBe:5ld2, PDBj:5ld2
PDBsum5ld2
PubMed27644322
UniProtP08394|RECB_ECOLI RecBCD enzyme subunit RecB (Gene Name=recB)

[Back to BioLiP]