Structure of PDB 7r76 Chain A Binding Site BS03

Receptor Information

>7r76 Chain A (length=1834) Species: 235443 (Cryptococcus neoformans var. grubii H99)

LDIKAAVRNMSDDLPPISDIEAMFDHLVSRIPDIVELVRQLNGRKLRVAT
MCSGTESPLLALNMIAKAIKAQHGLTLAFEHVFSCEIEPFKQAYIERNFT
PPILFRDVTELGKKRAHTAYGSMVDVPGDVDILIAGTSCVDGESGRTFRG
MLQWVKKHQPPIVILENVCNAPWDKVVEYFGQIDYDAQYTRLDTKEFYIP
HTRTRVYLFATPSSSESDDLPEKWAQTVKDLRRPWSSPFEAFLLHTDDPN
IHRARLELASARAQTRKTTDWNRCESRHQRARQDEALGLLRPLTSWQEAG
VCKGLDWTWNDWLLAQTERVVDLLEISTLRMAKDGIDSGFKACIWNVSQN
VDRQTGSSKTALAPCLTPNMIPWVTIRGGPVTGREALALQGIPVRELLLT
SENEDQLADLAGNAMTTTVVGSAMIAALKVACHKITEGANPEKEAALILE
KEAVDDEQVANRIIGEDYLEHHDLDLAKVTKLSEILDLACRSSRHCQCEG
QSGTAPNILECQECSYRACKSCGGRPEHVYAPCANQRVEPAEFEKRFKGL
LPMRVRIAGLTDQCLNAVRKAAEKSNKGSVNDNDWQLWSTALLEGIHDAE
FRFRYLKRQSTWTAVYEARRAMLSLVLRNQIPEWRLTIKAPASEPNNSQL
RALLLHPVARLQIDIAGQDVLCGPWELCIPSMKTIDIEITGKGELLPSWQ
ASLGLQGPFANTTRWSEVEISLQAEDENTLDRKLSGTYQLLPRCGQAMSS
LHKKRPDLSDDGLPQLYFFLDPTRCGESREDRYVFSTSTERLDYGTERPV
IARLDSHWREGNEKQRKVKLDVSGAWVKCPEAHLTAIRATFAIPSSASAI
SASLTTEGCSHAMALLSCRVPLDPTHSESMWRRGAWAEIDLSHQGNTTFA
NLAWITERLPPLDGLKNWAHIADDVSEHVCERCAPRPPKIHWITIIAFED
KLEAGQYEHALKHRPSPFVVQLRLDQDIGSFRIGLNIVSLAHRALSRLPP
TTSEHKISLSWRLTPGHVTESPQPRRVFILPSNKQDPENSQPEAFKLPLR
KEQLRSLWWMLEQEKATGKTHTFVEEEISESLLPAVGWRAEGKAERPVMV
RGGVIADQVGYGKTVISIALVAQTLSLPAPEPATPGLIDLKATLIVVPGH
LSKQWPNEIARFTGSMFKVIVIQGMKDLQEKTIAELGKADIIVMASEIFE
SDVYWSRLEYLSAQPREWLHDTQGGRFFCDRLDAAMESLVSQTKILKLLP
NPVLHMFRFRRVIADEFTYLQKKSLAAVLRLSSSYRWILSGTPPVSDFAA
IRSIATFMGIHLGVEDDGEGDVQYQKARAKDQTQAEKFHAFREVHSRAWH
NRRDELAQEFLNVFVRQNIIEDIPTVEHIHTFKLPASEGAVYLELEHHLQ
ALEMQARKETKFKNVSQGDRNARLEEALSDSKTAEEALLKRCCHFTLDLS
DKTQDAKSAQEACDHITSARARQLLACQEDLSRSVNQAIALHGWIKKKGG
FSKNDDERQPFAEWIAFSSNISKHQGDIEAARILLKVIEKCGVKDGNIPP
SPSDKQSPSGAKMDDVKWQLREQTHLLRKLVKELVARVRSLRFFEVVRKI
QKGKSDAQIVLESSECGHKEMAILSCCGHVACHKCMRKAAASQRCVKSCQ
AAVRPTNIVKVSSLGVEGELSSGRYGAKLEHLVNLIHSIPKNERVLVFLQ
WEDLAGKVSEALSAGRIPHVTLSGSAKSRANTLDRFQSTSARVLLLKMND
GSNLTTANHAVFLGPLFTNSLFNYRAVETQAIGRVRRYGQQKKVHIHRLL
ALDTIDMTIFNARRTELKEKTDWEEIPQEEYKGR

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: 7r76 Chain A Residue 2405

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7r76 Structural insights into DNMT5-mediated ATP-dependent high-fidelity epigenome maintenance.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): L2096 C2099 H2101
• Binding residue (residue number reindexed from 1): L1624 C1627 H1629
• 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:7r76, PDBe:7r76, PDBj:7r76
• PDBsum: 7r76
• PubMed: 35202575
• UniProt: J9VI03|DMT5_CRYNH DNA (cytosine-5-)-methyltransferase DMT5 (Gene Name=DMT5)