Structure of PDB 5ld2 Chain B Binding Site BS02

Receptor Information

>5ld2 Chain B (length=1151) Species: 83333 (Escherichia coli K-12)

AETLDPLRLPLQGERLIEASAGTGKTFTIAALYLRLLLGLGGSAAFPRPL
TVEELLVVTFTEAATAELRGRIRSNIHELRIACLRETTDNPLYERLLEEI
DDKAQAAQWLLLAERQMDEAAVFTIHGFCQRMLNLNAFESGMLFEQQLIE
DESLLRYQACADFWRRHCYPLPREIAQVVFETWKGPQALLRDINRYLQGE
APVIKAPPPDDETLASRHAQIVARIDTVKQQWRDAVGELDALIESSGIDR
RKFNRSNQAKWIDKISAWAEEETNSYQLPESLEKFTPRHPLFEAIDQLLA
EPLSIRDLVITRALAEIRETVAREKRRRGELGFDDMLSRLDSALRSESGE
VLAAAIRTRFPVAMIDEFQDTDPQQYRIFRRIWHHQPETALLLIGDPKQA
IYAFRGADIFTYMKARSEVHAHYTLDTNWRSAPGMVNSVNKLFSQTDDAF
MFREIPFIPVKSAGKNQALRFVFKGETQPAMKMWLMEGESCGVGDYQSTM
AQVCAAQIRDWLQAGQRGEALLMNGDDARPVRASDISVLVRSRQEAAQVR
DALTLLEIPSVYLSNRDSVFETLEAQEMLWLLQAVMTPERENTLRSALAT
SMMGLNALDIETLNNDEHAWDVVVEEFDGYRQIWRKRGVMPMLRALMSAR
NIAENLLATAGGERRLTDILHISELLQEAGTQLESEHALVRWLSQHILEP
DSNASSQQMRLESDKHLVQIVTIHKSKGLEYPLVWLPFITNFRVQEQAFY
HDRHSFEAVLDLNAAPESVDLAEAERLAEDLRLLYVALTRSVWHCSLGVA
PLVRRRGDKKGDTDVHQSALGRLLQKGEPQDAAGLRTCIEALCDDDIAWQ
TAQTGDNQPWQVNDVSTAELNAKTLQRLPGDNWRVTSYSGLQQRGAGAAA
AAAAAAAAAAAGAAPTLTPHQFPRGASPGTFLHSLFEDLDFTQPVDPNWV
REKLELGGFESQWEPVLTEWITAVLQAPLNETGVSLSQLSARNKQVEMEF
YLPISEPLIASQLDTLIRQFDPLSAGCPPLEFMQVRGMLKGFIDLVFRHE
GRYYLLAYKSNWLGEDSSAYTQQAMAAAMQAHRYDLQYQLYTLALHRYLR
HRIADYDYEHHFGGVIYLFLRGVDKEHPQQGIYTTRPNAGLIALMDEMFA
G

Ligand information

• Ligand ID: ANP
• InChI: InChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
• InChIKey: PVKSNHVPLWYQGJ-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.7.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
  CACTVS 3.370: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
  CACTVS 3.370: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
  ACDLabs 12.01: O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  OpenEye OEToolkits 1.7.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N
• Formula: C10 H17 N6 O12 P3
• Name: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
• ChEMBL: CHEMBL1230989
• ZINC: ZINC000008660410
• PDB chain: 5ld2 Chain B Residue 1501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5ld2 Mechanism for nuclease regulation in RecBCD.
• Resolution: 3.83 Å
• Binding residue (original residue number in PDB): G26 G28 K29 T30 F31 Q417 W447 R448 R808
• Binding residue (residue number reindexed from 1): G22 G24 K25 T26 F27 Q399 W429 R430 R790
• Annotation score: 3

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.

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

External links

• PDB: RCSB:5ld2, PDBe:5ld2, PDBj:5ld2
• PDBsum: 5ld2
• PubMed: 27644322
• UniProt: P08394|RECB_ECOLI RecBCD enzyme subunit RecB (Gene Name=recB)