Structure of PDB 6dc6 Chain A Binding Site BS01

Receptor Information
>6dc6 Chain A (length=992) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DIDEGLYSRQLYVLGHEAMKRLQTSSVLVSGLRGLGVEIAKNIILGGVKA
VTLHDQGTAQWADLSSQFYLREEDIGKNRAEVSQPRLAELNSYVPVTAYT
GPLVEDFLSGFQVVVLTNTPLEDQLRVGEFCHNRGIKLVVADTRGLFGQL
FCDFGEEMILTDSNGEQPLSAMVSMVTKDNPGVVTCLDEARHGFESGDFV
SFSEVQGMVELNGNQPMEIKVLGPYTFSICDTSNFSDYIRGGIVSQVKVP
KKISFKSLVASLAEPDFVVTDFAKFSRPAQLHIGFQALHQFCAQHGRPPR
PRNEEDAAELVALAQAVNARALPAVQQNNLDEDLIRKLAYVAAGDLAPIN
AFIGGLAAQEVMKACSGKFMPIMQWLYFDALECLPEDKEVLTEDKCLQRQ
NRYDGQVAVFGSDLQEKLGKQKYFLVGAGAIGCELLKNFAMIGLGCGEGG
EIIVTDMDTIEKSNLNRQFLFRPWDVTKLKSDTAAAAVRQMNPHIRVTSH
QNRVGPDTERIYDDDFFQNLDGVANALDNVDARMYMDRRCVYYRKPLLES
GTLGTKGNVQVVIPFLTESYSSSQDPPEKSIPIATLKNFPNAIEHTLQWA
RDEFEGLFKQPAENVNQYLTDPKFVERTLRLAGTQPLEVLEAVQRSLVLQ
RPQTWADCVTWACHHWHTQYSNNIRQLLHNFPPDQLTSSGAPFWSGPKRC
PHPLTFDVNNPLHLDYVMAAANLFAQTYGLTGSQDRAAVATFLQSVQVPE
FTPKSVDDSRLEELKATLPSPDKLPGFKMYPIDFEKDDDSNFHMDFIVAA
SNLRAENYDIPSADRHKSKLIAGKIIPAIATTTAAVVGLVCLELYKVVQG
HRQLDSYKNGFLNLALPFFGFSEPLAAPRHQYYNQEWTLWDRFEVQGLQP
NGEEMTLKQFLDYFKTEHKLEITMLSQGVSMLYSFFMPAAKLKERLDQPM
TEIVSRVSKRKLGRHVRALVLELCCNDESGEDVEVPYVRYTI
Ligand information
Ligand IDMG
InChIInChI=1S/Mg/q+2
InChIKeyJLVVSXFLKOJNIY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Mg+2]
CACTVS 3.341[Mg++]
FormulaMg
NameMAGNESIUM ION
ChEMBL
DrugBankDB01378
ZINC
PDB chain6dc6 Chain A Residue 1102 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6dc6 Crystal structure of a human ubiquitin E1-ubiquitin complex reveals conserved functional elements essential for activity.
Resolution3.14 Å
Binding residue
(original residue number in PDB)		D506 E509
Binding residue
(residue number reindexed from 1)		D458 E461
Annotation score4
Enzymatic activity
Catalytic site (original residue number in PDB) R57 R515 D576 A632 T633 K635
Catalytic site (residue number reindexed from 1) R9 R467 D528 A584 T585 K587
Enzyme Commision number 6.2.1.45: E1 ubiquitin-activating enzyme.
Gene Ontology
Molecular Function
GO:0003723 RNA binding
GO:0004839 ubiquitin activating enzyme activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008641 ubiquitin-like modifier activating enzyme activity
GO:0016874 ligase activity
Biological Process
GO:0006511 ubiquitin-dependent protein catabolic process
GO:0006974 DNA damage response
GO:0016567 protein ubiquitination
GO:0032446 protein modification by small protein conjugation
GO:0036211 protein modification process
Cellular Component
GO:0000792 heterochromatin
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005765 lysosomal membrane
GO:0005829 cytosol
GO:0010008 endosome membrane
GO:0030057 desmosome
GO:0030867 rough endoplasmic reticulum membrane
GO:0070062 extracellular exosome

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Molecular Function
View graph for
Biological Process
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Cellular Component
External links
PDB RCSB:6dc6, PDBe:6dc6, PDBj:6dc6
PDBsum6dc6
PubMed30279270
UniProtP22314|UBA1_HUMAN Ubiquitin-like modifier-activating enzyme 1 (Gene Name=UBA1)

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