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BioLiP

Structure of PDB 2zbk Chain B Binding Site BS01

Receptor Information

>2zbk Chain B (length=506) Species: 2286 (Saccharolobus shibatae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

EFFKRNPELAGFPNPARALYQTVRELIENSLDATDVHGILPNIKITIDLI
DDARQIYKVNVVDNGIGIPPQEVPNAFGRVLYSSKYVNRQTRGMYGLGVK
AAVLYSQMHQDKPIEIETSPVNSKRIYTFKLKIDINKNEPIIVERGSVEN
TRGFHGTSVAISIPGDWPKAKSRIYEYIKRTYIITPYAEFIFKDPEGNVT
YYPRLTNKIPKPPQEVKPHPYGVDREEIKILINNLKRDYTIKEFLVNEFQ
SIGDTTADKILELAGLKPNKKVKNLTEEEITRLVETFKKDEDFRSPSADS
LSVIGEDLIELGLKKIFNPDFAASITRKPKAYQGHPFIVEAGVAFGGSIP
VGEEPIVLRYANKIPLIYDEKSDVIWKVVEELDWKRYGIESDQYQMVVMV
HLCSTKIPYKSAGKESIAEVENIEKEIKNALMEVARKLKQYLSEKRKEQE
AKKKLLAYLKYIPEVSRSLATFLASGNKELVSKYQNEISEGLFKLISKKL
DLINIE

Ligand information

Ligand ID

RDC

InChI

InChI=1S/C18H17ClO6/c1-9-6-15-14(25-15)5-3-2-4-10(20)7-11-16(18(23)24-9)12(21)8-13(22)17(11)19/h2-5,8-9,14-15,21-22H,6-7H2,1H3/b4-2+,5-3-/t9-,14-,15-/m1/s1

InChIKey

WYZWZEOGROVVHK-GTMNPGAYSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.5.0	CC1CC2C(O2)C=CC=CC(=O)Cc3c(c(cc(c3Cl)O)O)C(=O)O1
OpenEye OEToolkits 1.5.0	C[C@@H]1C[C@@H]2[C@H](O2)\C=C/C=C/C(=O)Cc3c(c(cc(c3Cl)O)O)C(=O)O1
CACTVS 3.341	C[C@@H]1C[C@H]2O[C@@H]2\C=C/C=C/C(=O)Cc3c(Cl)c(O)cc(O)c3C(=O)O1
ACDLabs 10.04	O=C2C=CC=CC3OC3CC(OC(=O)c1c(O)cc(O)c(Cl)c1C2)C
CACTVS 3.341	C[CH]1C[CH]2O[CH]2C=CC=CC(=O)Cc3c(Cl)c(O)cc(O)c3C(=O)O1

Formula

C18 H17 Cl O6

Name

RADICICOL;
MONORDEN

PDB chain

2zbk Chain B Residue 531 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	2zbk Crystal Structure of an Intact Type II DNA Topoisomerase: Insights into DNA Transfer Mechanisms
Resolution	3.56 Å
Binding residue (original residue number in PDB)	D76 G80 I81 V112 T170 V172
Binding residue (residue number reindexed from 1)	D63 G67 I68 V99 T157 V159
Annotation score	1
Binding affinity	PDBbind-CN: -logKd/Ki=5.70,Kd=2uM

Enzymatic activity

Enzyme Commision number

5.6.2.2: DNA topoisomerase (ATP-hydrolyzing).

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:0005515	protein binding
GO:0005524	ATP binding
GO:0042802	identical protein binding

	Biological Process
GO:0006265	DNA topological change
GO:0006268	DNA unwinding involved in DNA replication

	Cellular Component
GO:0009330	DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex

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Molecular Function

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Cellular Component

External links

PDB	RCSB:2zbk, PDBe:2zbk, PDBj:2zbk
PDBsum	2zbk
PubMed	18334211
UniProt	O05207\|TOP6B_SACSH Type 2 DNA topoisomerase 6 subunit B (Gene Name=top6B)

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