Structure of PDB 5bk4 Chain D Binding Site BS03

Receptor Information

>5bk4 Chain D (length=661) Species: 4932 (Saccharomyces cerevisiae)

SFDRPEIYSAPVLQGESPNDDDNTEIIKSFKNFILEFRLDSQFIYRDQLR
NNILVKNYSLTVNMEHLIGYNEDIYKKLSDEPSDIIPLFETAITQVAKRI
SILSRAQSANSLPTFQLILNSNANQIPLRDLDSEHVSKIVRLSGIIISTS
VLSSRATYLSIMCRNCRHTTSITINNFNSITGNTVSLPRSCLSTIESESS
MANESNIGDESTKKNCGPDPYIIIHESSKFIDQQFLKLQEIPELVPVGEM
PRNLTMTCDRYLTNKVIPGTRVTIVGIYSIYNSKNGSGVAIRTPYIKILG
IQSDVETSSIWNSVTMFTEEEEEEFLQLSRNPKLYEILTNSIAPSIFGNE
DIKKAIVCLLMGGSKKILPDGMRLRGDINVLLLGDPGTAKSQLLKFVEKV
SPIAVYTSGKGSSAAGLTASVQRDPMTREFYLEGGAMVLADGGVVCIDEF
DKMRDEDRVAIHEAMEQQTISIAKAGITTVLNSRTSVLAAANPIYGRYDD
LKSPGDNIDFQTTILSRFDMIFIVKDDHNEERDISIANHVINIHTGNANA
MQNQQEENGSEISIEKMKRYITYCRLKCAPRLSPQAAEKLSSNFVTIRKQ
LLINELESTERSSIPITIRQLEAIIRITESLAKLELSPIAQERHVDEAIR
LFQASTMDAAS

Ligand information

• Ligand ID: ADP
• InChI: InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
• InChIKey: XTWYTFMLZFPYCI-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
• Formula: C10 H15 N5 O10 P2
• Name: ADENOSINE-5'-DIPHOSPHATE
• ChEMBL: CHEMBL14830
• DrugBank: DB16833
• ZINC: ZINC000012360703
• PDB chain: 5bk4 Chain D Residue 2001

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5bk4 Cryo-EM structure of Mcm2-7 double hexamer on DNA suggests a lagging-strand DNA extrusion model.
• Resolution: 3.9 Å
• Binding residue (original residue number in PDB): S377 F379 G419 A421 K422 S423 I568
• Binding residue (residue number reindexed from 1): S345 F347 G387 A389 K390 S391 I536
• Annotation score: 5

Enzymatic activity

• Enzyme Commision number: 3.6.4.12: DNA helicase.

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003682 chromatin binding
• GO:0003688 DNA replication origin binding
• GO:0003697 single-stranded DNA binding
• GO:0004386 helicase activity
• GO:0005515 protein binding
• GO:0005524 ATP binding
• GO:0008270 zinc ion binding
• GO:0016787 hydrolase activity
• GO:0016887 ATP hydrolysis activity
• GO:0017116 single-stranded DNA helicase activity
• GO:0043138 3'-5' DNA helicase activity

Biological Process

• GO:0000727 double-strand break repair via break-induced replication
• GO:0006260 DNA replication
• GO:0006267 pre-replicative complex assembly involved in nuclear cell cycle DNA replication
• GO:0006268 DNA unwinding involved in DNA replication
• GO:0006270 DNA replication initiation
• GO:0006279 premeiotic DNA replication
• GO:0006368 transcription elongation by RNA polymerase II
• GO:0030174 regulation of DNA-templated DNA replication initiation
• GO:0031507 heterochromatin formation
• GO:0031509 subtelomeric heterochromatin formation
• GO:0032508 DNA duplex unwinding
• GO:0033260 nuclear DNA replication

Cellular Component

• GO:0000781 chromosome, telomeric region
• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0005656 nuclear pre-replicative complex
• GO:0005737 cytoplasm
• GO:0031261 DNA replication preinitiation complex
• GO:0031298 replication fork protection complex
• GO:0042555 MCM complex
• GO:0043596 nuclear replication fork
• GO:0071162 CMG complex

External links

• PDB: RCSB:5bk4, PDBe:5bk4, PDBj:5bk4
• PDBsum: 5bk4
• PubMed: 29078375
• UniProt: P29496|MCM5_YEAST Minichromosome maintenance protein 5 (Gene Name=MCM5)