Structure of PDB 7r77 Chain A Binding Site BS07

Receptor Information

>7r77 Chain A (length=1830) Species: 235443 (Cryptococcus neoformans var. grubii H99)

DIKAAVRNMSDDLPPISDIEAMFDHLVSRIPDIVELVRQLNGRKLRVATM
CSGTESPLLALNMIAKAIKAQHGLTLAFEHVFSCEIEPFKQAYIERNFTP
PILFRDVTELGKKRAHTAYGSMVDVPGDVDILIAGTSCVDYSSGRTFRGM
LQWVKKHQPPIVILENVCNAPWDKVVEYFGQIDYDAQYTRLDTKEFYIPH
TRTRVYLFATPSDLPEKWAQTVKDLRRPWSSPFEAFLLHTDDPNIHRARL
ELASARAQTSRKTTDWNRCESRHQRARQDEALGLLRPLTSWQEAGVCKGL
DWTWNDWLLAQTERVVDLLEISTLRMAKDGIDSGFKACIWNVSQNVDRQT
GSSKTALAPCLTPNMIPWVTIRGGPVTGREALALQGIPVRELLLTSENED
QLADLAGNAMTTTVVGSAMIAALKVACHKITEGANPEKEAALILEKEAVD
DEQVANRIIGEDYLEHHDLDLAKVTKSNLSEILDLACRSSRHCQCEGQSG
TAPNILECQECSYRACKSCGGRPEHVYAPCANQRVEPAEFEKRFKGLLPM
RVRIAGLTDQCLNAVRKAAEKSNKGSVNDNDWQLWSTALLEGIHDAEFRF
RYLKRQSTWTAVYEARRAMLSLVLRNQIPEWRLTIKAPASEPNNSQLRAL
LLHPVARLQIDIAGQDVLCGPWELCIPSMKTIDIEITGKGELLPSWQASL
GLQGPFANTTRWSEVEISLQAEDENTLDRKLSGTYQLLPRCGQAMSSLHK
KRPDLSDDGLPQLYFFLDPTRCGESREDRYVFSTSTERLDYGTERPVIAR
LDSHWREGNEKQRKVKLDVSGAWVKCPEAHLTAIRATFAIPSSASAISAS
LTTEGCSHAMALLSCRVPLDPTHSESMWRRGAWAEIDLSHQGNTTFANLA
WITERLPPLDGLKNWAHIADDVSEHVCERCAPRPPKIHWIKTIIAFEDKL
EAGQYEHALKHRPSPFVVQLRLDQDIGSFRIGLNIVSLAHRALSRLPPTT
SEHKISLSWRLTPGHVTESPQPRRVFILPSNKQDPENSQFKLPLRKEQLR
SLWWMLEQEKATGKTHTFVEEEISESLLPAVGWRAEGKAERPVMVRGGVI
ADQVGYGKTVISIALVAQTLSLPAPEPATPGLIDLKATLIVVPGHLSKQW
PNEIARFTGSMFKVIVIQGMKDLQEKTIAELGKADIIVMASEIFESDVYW
SRLEYLSAQPREWLHDTQGGRFFCDRLDAAMESLVSQTKILKLLPNPVLH
MFRFRRVIADEFTYLQKKSLAAVLRLSSSYRWILSGTPPVSDFAAIRSIA
TFMGIHLGVEDDGEGDVQYQKARAKDQTQAEKFHAFREVHSRAWHNRRDE
LAQEFLNVFVRQNIAEIEDIPTVEHIHTFKLPASEGAVYLELEHHLQALE
MQARKETKFKNVSQGDRNARLEEALSDSKTAEEALLKRCCHFTLDLSDKT
QDAKSAQEACDHITSARARQLLACQEDLSRSVNQAIALHGWIKKKGGFRQ
PFAEWIAFSSNISKHQGDIEAARILLKVIEKCGVKDGNIPPSPSDKQSPS
KMDDVKWQLREQTHLLRKLVKELVARVRSLRFFEVVRKIQKGKSDAQIVL
ESSECGHKPSTNPDIEMAILSCCGHVACHKCMRKAAASQRCVKSGECQAA
VRPTNIVKVSSLGVEGELSSGRYGAKLEHLVNLIHSIPKNERVLVFLQWE
DLAGKVSEALSAGRIPHVTLSGSAKSRANTLDRFQADSARVLLLKMNDSN
LTTANHAVFLGPLFTNSLFNYRAVETQAIGRVRRYGQQKKVHIHRLLALD
TIDMTIFNARRTELKEKTDWEEIPQEEYKG

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: 7r77 Chain A Residue 2405

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7r77 Structural insights into DNMT5-mediated ATP-dependent high-fidelity epigenome maintenance.
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): C2099 H2101 C2123
• Binding residue (residue number reindexed from 1): C1623 H1625 C1647
• 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:7r77, PDBe:7r77, PDBj:7r77
• PDBsum: 7r77
• PubMed: 35202575
• UniProt: J9VI03|DMT5_CRYNH DNA (cytosine-5-)-methyltransferase DMT5 (Gene Name=DMT5)