Structure of PDB 7r78 Chain A Binding Site BS07

Receptor Information

>7r78 Chain A (length=1880) Species: 235443 (Cryptococcus neoformans var. grubii H99)

DDLPPISDIEAMFDHLVSRIPDIVELVRQLNGRKLRVATMCSGTESPLLA
LNMIAKAIKAQHGLTLAFEHVFSCEIEPFKQAYIERNFTPPILFRDVTEL
GKKRAHTAYGSMVDVPGDVDILIAGTSCVDYSNLNNVQQDIDANGESGRT
FRGMLQWVKKHQPPIVILENVCNAPWDKVVEYFGQIDYDAQYTRLDTKEF
YIPHTRTRVYLFATPSSSESDDLPEKWAQTVKDLRRPWSSPFEAFLLHTD
DPNIHRARLELASARAGTSRKTTDWNRCESRHQRARQDEALGLLRPLTSW
QEAGVCKGLDWTWNDWLLAQTERVVDLLEISTLRMAKDGIDSGFKACIWN
VSQNVDRQTGSSKTALAPCLTPNMIPWVTIRGGPVTGREALALQGIPVRE
LLLTSENEDQLADLAGNAMTTTVVGSAMIAALKVACHKITEGANPEKEAA
LILEKEAVDDEQVANRIIGEDYLEHHDLDLAKVTKSNLSEILDLACRSSR
HCQCEGQSGTAPNILECQECSYRACKSCGGRPEHVYAPCANQRVEPAEFE
KRFKGLLPMRVRIAGLTDQCLNAVRKAAEKSNKGSVNDNDWQLWSTALLE
GIHDAEFRFRYLKRQSTWTAVYEARRAMLSLVLRNQIPEWRLTIKAPASE
PNNSQLRALLLHPVARLQIDIAGQDVLCGPWELCIPSMKTIDIEITGKGE
LLPSWQASLGLQGPFANTTRWSEVEISLQAEDENTLDRKLSGTYQLLPRC
GQAMSSLHKKRPDLSDDGLPQLYFFLDPTRCGESREDRYVFSTSTERLDY
GTERPVIARLDSHWREGNEKQRKVKLDVSGAWVKCPEAHLTAIRATFAIP
SSASAISASLTTEGCSHAMALLSCRVPLDPTHSESMWRRGAWAEIDLSHQ
GNTTFANLAWITERLPPLDGLKNWAHIADDVSEHVCERCAPRPPKIHWIK
RAFEDKLEAGQYEHALKHRPSPFVVQLRLDQDIGSFRIGLNIVSLAHRAL
SRLPPTTSEHKISLSWRLTPGHVTESPQPRRVFILPSNKQDPENSQPEAF
KLPLRKEQLRSLWWMLEQEKATGKTHTFVEEEISESLLPAVGWRAEGKAE
RPVMVRGGVIADQVGYGKTVISIALVAQTLSLPAPEPATPGLIDLKATLI
VVPGHLSKQWPNEIARFTGSMFKVIVIQGMKDLQEKTIAELGKADIIVMA
SEIFESDVYWSRLEYLSAQPREWLHDTQGGRFFCDRLDAAMESLVSQTKI
LKEKGSEAAMRAMEDKKKSLVDNVGSKKEVHTKLLPNPVLHMFRFRRVIA
DEFTYLQKKSLAAVLRLSSSYRWILSGTPPVSDFAAIRSIATFMGIHLGV
EDDGEGDDQTQAEKFHAFREVHSRAWHNRRDELAQEFLNVFVRQNIAEIE
DIPTVEHIHTFKLPASEGAVYLELEHHLQALEMQARKENVSQGDRNARLE
EALSDSKTAEEALLKRCCHFTLDLSDKTQDAKSAQEACDHITSARARQLL
ACQEDLSRSVNQAIALHGWIKKKGGFSKNDDERQPFAEWIAFSSNISKHQ
GDIEAARILLKVIEKCGVKDGNIPPSPSDKQSPSIASGAKMDDVKWQLRE
QTHLLRKLVKELVARVRSLRFFEVVRKIQKGKSDAQIVLESSECGHKPST
NPDIEMAILSCCGHVACHKCMRKAAASQRCVKSGECQAAVRPTNIVKVSS
LGVEGELSSGRYGAKLEHLVNLIHSIPKNERVLVFLQWEDLAGKVSEALS
AGRIPHVTLSGSAKSRANTLDRFQSTNADSARVLLLKMNDASAAGSNLTT
ANHAVFLGPLFTNSLFNYRAVETQAIGRVRRYGQQKKVHIHRLLALDTID
MTIFNARRTELKEKTDWEEIPQEEYKGRGS

Ligand information

• Ligand ID: ZN
• InChI: InChI=1S/Zn/q+2
• InChIKey: PTFCDOFLOPIGGS-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: [Zn++]
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Zn+2]
• Formula: Zn
• Name: ZINC ION
• ChEMBL: CHEMBL1236970
• DrugBank: DB14532
• PDB chain: 7r78 Chain A Residue 2405

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7r78 Structural insights into DNMT5-mediated ATP-dependent high-fidelity epigenome maintenance.
• Resolution: 3.5 Å
• Binding residue (original residue number in PDB): C2081 A2103 C2104
• Binding residue (residue number reindexed from 1): C1644 A1666 C1667
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 3.6.4.-

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003682 chromatin binding
• GO:0003886 DNA (cytosine-5-)-methyltransferase activity
• GO:0005524 ATP binding
• GO:0008094 ATP-dependent activity, acting on DNA
• GO:0008168 methyltransferase activity
• GO:0016787 hydrolase activity
• GO:0016887 ATP hydrolysis activity
• GO:0043565 sequence-specific DNA binding
• GO:0120328 ATP-dependent DNA (cytosine-5-)-methyltransferase activity
• GO:0140658 ATP-dependent chromatin remodeler activity

Biological Process

• GO:0006289 nucleotide-excision repair
• GO:0006338 chromatin remodeling
• GO:0006346 DNA methylation-dependent heterochromatin formation
• GO:0009889 regulation of biosynthetic process
• GO:0032259 methylation

Cellular Component

• GO:0005634 nucleus
• GO:0005694 chromosome

External links

• PDB: RCSB:7r78, PDBe:7r78, PDBj:7r78
• PDBsum: 7r78
• PubMed: 35202575
• UniProt: J9VI03|DMT5_CRYNH DNA (cytosine-5-)-methyltransferase DMT5 (Gene Name=DMT5)