Structure of PDB 4ddt Chain A Binding Site BS02

Receptor Information
>4ddt Chain A (length=1102) Species: 2336 (Thermotoga maritima) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AVNSKYHHSCINCGGLNTDERNERGLPCEVCLPEDSPSDIYRALLERKTL
KEYRFYHEFWNEYEDFRSFFKKKFGKDLTGYQRLWAKRIVQGKSFTMVAP
TGVGKTTFGMMTALWLARKGKKSALVFPTVTLVKQTLERLQKLADEKVKI
FGFYSSMKKEEKEKFEKSFEEDDYHILVFSTQFVSKNREKLSQKRFDFVF
VDDVDAVLKASRNIDTLLMMVGIPEEIIRKAFSTIKQGKIYERPKNLKPG
ILVVSSATAKPRGIRPLLFRDLLNFTVGRLVSVARNITHVRISSRSKEKL
VELLEIFRDGILIFAQTEEEGKELYEYLKRFKFNVGETWSEFEKNFEDFK
VGKINILIGVQAYYGKLTRGVDLPERIKYVIFWGTPSMRFSLELDKAPRF
VLARVLKEMGLIKAQENPDVEELRKIAKEHLTQKEFVEKVKEMFRGVVVK
DEDLELIIPDVYTYIQASGRSSRILNGVLVKGVSVIFEEDEEIFESLKTR
LLLIAEEEIIEEAEANWKELVHEVEESRRRSERELTDTSRSLLIIVESPT
KAETLSRFLGRASSRKERNIIVHEAVTGEGVILFTATRGHVYDLVTKGGI
HGVEEENGKFVPVYNSLKRCRDCGYQFTEDRDECPVCSSKNIDDKTETLR
ALREISLEADEILVATDPDVEGEKISWDVTQYLLPSTRSLRRIEMHEITR
YGFKKARESVRFVDFNLVKAQIVRRVQDRWIGFELSGKLQKRFGRSNLSA
GRVQSTVLGWIVEREEEYKKSEKDFTLLVLENGVNLEVEGKIADDVVTVV
ELQEAEEEKNPLPPYTTSSALSEISQKLRLGVQEVMDILQDLFEKGFITY
HRTDSTRISLEGQNVARTYLRKIGKEDIFMGRSWSTEGAHEAIRPVKPID
ARELEEMIEEGLIADLTKKHLRVYELIFNRFLASQSAAVKVKKQIVTVDV
DGKRMGIEQIVEILRDGWNLFVPLTVSPRFEHRTYKIKEKKFYKKHTVPL
FTQASIVEEMKKRGIGRPSTYAKIVEVLFRRGYVYEDKYKRVRPTRFGVM
VYSYLKERYEKYVTEETTRRLEEIMDKVERGEEDYQATLRLLYEEIKSLM
EE
Ligand information
Ligand IDZN
InChIInChI=1S/Zn/q+2
InChIKeyPTFCDOFLOPIGGS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341[Zn++]
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Zn+2]
FormulaZn
NameZINC ION
ChEMBLCHEMBL1236970
DrugBankDB14532
ZINC
PDB chain4ddt Chain A Residue 1202 [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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PDB4ddt Crystal structures of Thermotoga maritima reverse gyrase: inferences for the mechanism of positive DNA supercoiling.
Resolution3.2 Å
Binding residue
(original residue number in PDB)		C11 C14 C29 C32
Binding residue
(residue number reindexed from 1)		C10 C13 C28 C31
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) E548 S549 D668 D670 E672 Y851 R853 H891
Catalytic site (residue number reindexed from 1) E547 S548 D667 D669 E671 Y850 R852 H890
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

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4ddt, PDBe:4ddt, PDBj:4ddt
PDBsum4ddt
PubMed23209025
UniProtO51934|RGYR_THEMA Reverse gyrase (Gene Name=rgy)

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