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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

3CMM

Crystal Structure of the Uba1-Ubiquitin Complex

Functional Information from GO Data
ChainGOidnamespacecontents
A0000166molecular_functionnucleotide binding
A0004839molecular_functionubiquitin activating enzyme activity
A0005515molecular_functionprotein binding
A0005524molecular_functionATP binding
A0005634cellular_componentnucleus
A0005737cellular_componentcytoplasm
A0006511biological_processubiquitin-dependent protein catabolic process
A0006974biological_processDNA damage response
A0008641molecular_functionubiquitin-like modifier activating enzyme activity
A0016567biological_processprotein ubiquitination
A0016874molecular_functionligase activity
A0036211biological_processprotein modification process
A0046872molecular_functionmetal ion binding
C0000166molecular_functionnucleotide binding
C0004839molecular_functionubiquitin activating enzyme activity
C0005515molecular_functionprotein binding
C0005524molecular_functionATP binding
C0005634cellular_componentnucleus
C0005737cellular_componentcytoplasm
C0006511biological_processubiquitin-dependent protein catabolic process
C0006974biological_processDNA damage response
C0008641molecular_functionubiquitin-like modifier activating enzyme activity
C0016567biological_processprotein ubiquitination
C0016874molecular_functionligase activity
C0036211biological_processprotein modification process
C0046872molecular_functionmetal ion binding
Functional Information from PDB Data
site_idAC1
Number of Residues2
DetailsBINDING SITE FOR RESIDUE PRO A 5119
ChainResidue
AASP316
AASN320
site_idAC2
Number of Residues4
DetailsBINDING SITE FOR RESIDUE PRO C 5129
ChainResidue
CASP316
CASN320
CILE323
CLYS349
Functional Information from PROSITE/UniProt
site_idPS00299
Number of Residues26
DetailsUBIQUITIN_1 Ubiquitin domain signature. KskIqDkegIPpdqQrLIFaGkqleD
ChainResidueDetails
BLYS27-ASP52
site_idPS00536
Number of Residues9
DetailsUBIQUITIN_ACTIVAT_1 Ubiquitin-activating enzyme signature 1. KACSGKFtP
ChainResidueDetails
ALYS376-PRO384
site_idPS00865
Number of Residues9
DetailsUBIQUITIN_ACTIVAT_2 Ubiquitin-activating enzyme active site. PLCTLRsFP
ChainResidueDetails
APRO598-PRO606
Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues274
DetailsRepeat: {"description":"1-1"}
ChainResidueDetails
site_idSWS_FT_FI2
Number of Residues308
DetailsRepeat: {"description":"1-2"}
ChainResidueDetails
site_idSWS_FT_FI3
Number of Residues1104
DetailsRegion: {"description":"2 approximate repeats"}
ChainResidueDetails
site_idSWS_FT_FI4
Number of Residues2
DetailsActive site: {"description":"Glycyl thioester intermediate","evidences":[{"source":"PROSITE-ProRule","id":"PRU10132","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"24816100","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
site_idSWS_FT_FI5
Number of Residues14
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"35970836","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"7ZH9","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI6
Number of Residues10
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"35970836","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"24816100","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"7ZH9","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI7
Number of Residues2
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"17287358","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI8
Number of Residues2
DetailsModified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18407956","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI9
Number of Residues6
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"22106047","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails
site_idSWS_FT_FI10
Number of Residues150
DetailsDomain: {"description":"Ubiquitin-like 5","evidences":[{"source":"PROSITE-ProRule","id":"PRU00214","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI11
Number of Residues12
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"UniProtKB","id":"P0CG47","evidenceCode":"ECO:0000250"}]}
ChainResidueDetails
site_idSWS_FT_FI12
Number of Residues4
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)","evidences":[{"source":"PROSITE-ProRule","id":"PRU00214","evidenceCode":"ECO:0000255"}]}
ChainResidueDetails
site_idSWS_FT_FI13
Number of Residues2
DetailsCross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"7862120","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails
Catalytic Information from CSA
site_idMCSA1
Number of Residues8
DetailsM-CSA 307
ChainResidueDetails
AARG21electrostatic stabiliser, hydrogen bond donor, steric role
AARG481electrostatic stabiliser, hydrogen bond donor, steric role
AASP544steric role
ACYS600activator, covalently attached, hydrogen bond donor, nucleophile, proton donor
ATHR601hydrogen bond acceptor, hydrogen bond donor, increase acidity, increase nucleophilicity, proton acceptor, proton donor, proton relay
AARG603electrostatic stabiliser, hydrogen bond donor
AASN781electrostatic stabiliser, hydrogen bond donor
AASP782electrostatic stabiliser, hydrogen bond donor
site_idMCSA2
Number of Residues5
DetailsM-CSA 939
ChainResidueDetails
ACYS600nucleofuge
ATHR601modifies pKa
AARG603electrostatic stabiliser
AASN781electrostatic stabiliser
AASP782electrostatic stabiliser
site_idMCSA3
Number of Residues8
DetailsM-CSA 307
ChainResidueDetails
BTHR12electrostatic stabiliser, hydrogen bond donor, steric role
site_idMCSA4
Number of Residues5
DetailsM-CSA 939
ChainResidueDetails

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PDB entries from 2025-12-10

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