Structure of PDB 1gl9 Chain B Binding Site BS01

Receptor Information
>1gl9 Chain B (length=1020) Species: 224325 (Archaeoglobus fulgidus DSM 4304) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IPVVYPVCGGLESKEIEKHKRSLCLFPEDFLLKEFVEFFRKCVGEPRAIQ
KMWAKRILRKESFAATAPTGVGKTSFGLAMSLFLALKGKRCYVIFPTSLL
VIQAAETIRKYAEKAGVGTENLIGYYHGRIPKREKENFMQNLRNFKIVIT
TTQFLSKHYRELGHFDFIFVDDVDAILKASKNVDKLLHLLGFHYDLKTKS
WVGEARGCLMVSTATAKKGKKAELFRQLLNFDIGSSRITVRNVEDVAVND
ESISTLSSILEKLGTGGIIYARTGEEAEEIYESLKNKFRIGIVTATKKGD
YEKFVEGEIDHLIGTAHYYGTLVRGLDLPERIRFAVFVGCPSFRVTIEDI
DSLSPQMVKLLAYLYRNVDEIERLLPAVERHIDEVREILKKVMGKERPQA
KDVVVREGEVIFPDLRTYIQGSGRTSRLFAGGLTKGASFLLEDDSELLSA
FIERAKLYDIEFKSIDEVDFEKLSRELDESRDRYRRRQEFDLIKPALFIV
ESPTKARQISRFFGKPSVKVLDGAVVYEIPMQKYVLMVTASIGHVVDLIT
NRGFHGVLVNGRFVPVYASIKVDNSRSRIEALRKLAHDAEFVIVGTDPDT
EGEKIAWDLKNLLSGCGAVKRAEFHEVTRRAILEALESLRDVDENLVKAQ
VVRRIEDRWIGFVLSQKLWERFNNRNLSAGRAQTLVLGWIIDRFQESRER
RKIAIVRDFDLVLEHDEEEFDLTIKLVEEREELRTPLPPYTTETMLSDAN
RILKFSVKQTMQIAQELFENGLITYHRTDSTRVSDVGQRIAKEYLGDDFV
GREWGESGAHECIRPTRPLTRDDVQRLIQEGVLVVEGLRWEHFALYDLIF
RRFMASQCRPFKVVVKKYSIEFDGKTAEEERIVRAEGRAYELYRAVWVKN
ELPTGTFRVKAEVKSVPKVLPFTQSEIIQMMKERGIGRPSTYATIVDRLF
MRNYVVEKYGRMIPTKLGIDVFRFLVRRYAKFVSEDRTRDLESRMDAIER
GELDYLKALEDMYAEIKSID
Ligand information
Ligand IDANP
InChIInChI=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
InChIKeyPVKSNHVPLWYQGJ-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(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 12.01O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.0c1nc(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
FormulaC10 H17 N6 O12 P3
NamePHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
ChEMBLCHEMBL1230989
DrugBank
ZINCZINC000008660410
PDB chain1gl9 Chain B Residue 2055 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB1gl9 Crystal Structure of Reverse Gyrase: Insights Into the Positive Supercoiling of DNA.
Resolution3.2 Å
Binding residue
(original residue number in PDB)		V54 E56 Q61 G81 V82 G83 K84 T85 S86 R498 Q499
Binding residue
(residue number reindexed from 1)		V43 E45 Q50 G70 V71 G72 K73 T74 S75 R487 Q488
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) E512 D631 D633 E635 Y809 R811 H844
Catalytic site (residue number reindexed from 1) E501 D597 D599 E601 Y775 R777 H810
Enzyme Commision number 5.6.2.-
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003916 DNA topoisomerase activity
GO:0003918 DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
GO:0005524 ATP binding
GO:0008094 ATP-dependent activity, acting on DNA
GO:0008270 zinc ion binding
GO:0016887 ATP hydrolysis activity
GO:0046872 metal ion binding
GO:0160097 reverse gyrase activity
Biological Process
GO:0006265 DNA topological change
GO:0006268 DNA unwinding involved in DNA replication
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1gl9, PDBe:1gl9, PDBj:1gl9
PDBsum1gl9
PubMed11823434
UniProtO29238|RGYR_ARCFU Reverse gyrase (Gene Name=rgy)

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