Structure of PDB 2xcr Chain D

Receptor sequence

>2xcrD (length=719) Species: 158879 (Staphylococcus aureus subsp. aureus N315)

GKLADCSSKSPEECEIFLVEGDSAGGSTKSGRDSRTQAILPLRGKILNVE
KARLDRILNNNEIRQMITAFGTGIGGDFDLAKARYHKIVIMTDADVDGAH
IRTLLLTFFYRFMRPLIEAGYVYIAQPPLYKLTQGKQKYYVYNDRELDKL
KSELNPTPKWSIARYKGLGEMNADQLWETTMNPEHRALLQVKLEDAIEAD
QTFEMLMGDVVENRRQFIEDNAVYANLDFAELPQSRINERNITSEMRESF
LDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKSARIVG
DVMGKYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDGAAAMR
FTEARMTKITLELLRDINKDTIDFIDNYDGNEREPSVLPARFPNLLANGA
SGIAVGMATNIPPHNLTELINGVLSLSKNPDISIAELMEDIEGPDFPTAG
LILGKSGIRRAYETGRGSIQMRSRAVIEERGGGRQRIVVTEIPFQVNKAR
MIEKIAELVRDKKIDGITDLRDETSLRTGVRVVIDVRKDANASVILNNLY
KQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVRRRTQYNLR
KAKDRAHILEGLRIALDHIDEIISTIRESDTDKVAMESLQQRFKLSEKQA
QAILDMRLRRLTGLERDKIEAEYNELLNYISELETILADEEVLLQLVRDE
LTEIRDRFGDDRRTEIQLG

3D structure

• PDB: 2xcr Type Iia Topoisomerase Inhibition by a New Class of Antibacterial Agents.
• Chain: D
• Resolution: 3.5 Å

Enzymatic activity

• Enzyme Commision number: 5.6.2.2: DNA topoisomerase (ATP-hydrolyzing).

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	D	K460 L462 N463 K466 R471 H515 V626 R629 R1122 I1175 G1178 M1179 A1180 R1238	K45 L47 N48 K51 R56 H100 V211 R214 R350 I403 G406 M407 A408 R466
BS02	dna	D	G436 D437 S438 R458 G459 K460 R1033 K1043 V1045 H1046 H1079 H1081 G1082 S1085 R1092	G21 D22 S23 R43 G44 K45 R261 K271 V273 H274 H307 H309 G310 S313 R320
BS03	RXV	D	A1068 D1083 M1121	A296 D311 M349

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003918 DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
• GO:0005524 ATP binding

Biological Process

• GO:0006259 DNA metabolic process
• GO:0006265 DNA topological change

External links

• PDB: RCSB:2xcr, PDBe:2xcr, PDBj:2xcr
• PDBsum: 2xcr
• PubMed: 20686482
• UniProt: P66937|GYRB_STAAN DNA gyrase subunit B (Gene Name=gyrB);
  Q99XG5|GYRA_STAAN DNA gyrase subunit A (Gene Name=gyrA)