Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6DC6

Crystal structure of human ubiquitin activating enzyme E1 (Uba1) in complex with ubiquitin

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0000792	cellular_component	heterochromatin
A	0003723	molecular_function	RNA binding
A	0004839	molecular_function	ubiquitin activating enzyme activity
A	0005515	molecular_function	protein binding
A	0005524	molecular_function	ATP binding
A	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0005737	cellular_component	cytoplasm
A	0005739	cellular_component	mitochondrion
A	0005765	cellular_component	lysosomal membrane
A	0005829	cellular_component	cytosol
A	0006511	biological_process	ubiquitin-dependent protein catabolic process
A	0006974	biological_process	DNA damage response
A	0008641	molecular_function	ubiquitin-like modifier activating enzyme activity
A	0010008	cellular_component	endosome membrane
A	0016567	biological_process	protein ubiquitination
A	0016874	molecular_function	ligase activity
A	0030057	cellular_component	desmosome
A	0030867	cellular_component	rough endoplasmic reticulum membrane
A	0036211	biological_process	protein modification process
A	0070062	cellular_component	extracellular exosome
C	0000166	molecular_function	nucleotide binding
C	0000792	cellular_component	heterochromatin
C	0003723	molecular_function	RNA binding
C	0004839	molecular_function	ubiquitin activating enzyme activity
C	0005515	molecular_function	protein binding
C	0005524	molecular_function	ATP binding
C	0005634	cellular_component	nucleus
C	0005654	cellular_component	nucleoplasm
C	0005737	cellular_component	cytoplasm
C	0005739	cellular_component	mitochondrion
C	0005765	cellular_component	lysosomal membrane
C	0005829	cellular_component	cytosol
C	0006511	biological_process	ubiquitin-dependent protein catabolic process
C	0006974	biological_process	DNA damage response
C	0008641	molecular_function	ubiquitin-like modifier activating enzyme activity
C	0010008	cellular_component	endosome membrane
C	0016567	biological_process	protein ubiquitination
C	0016874	molecular_function	ligase activity
C	0030057	cellular_component	desmosome
C	0030867	cellular_component	rough endoplasmic reticulum membrane
C	0036211	biological_process	protein modification process
C	0070062	cellular_component	extracellular exosome

Functional Information from PDB Data

site_id	AC1
Number of Residues	2
Details	binding site for residue MG A 1101

Chain	Residue
A	ASP576
A	POP1103

site_id	AC2
Number of Residues	3
Details	binding site for residue MG A 1102

Chain	Residue
A	ASP506
A	GLU509
A	POP1103

site_id	AC3
Number of Residues	9
Details	binding site for residue POP A 1103

Chain	Residue
A	GLN516
A	LYS528
A	ASP576
A	MG1101
A	MG1102
A	ARG57
A	ASP506
A	ASN512
A	ARG515

site_id	AC4
Number of Residues	2
Details	binding site for residue MG C 1101

Chain	Residue
C	ASP576
C	POP1103

site_id	AC5
Number of Residues	4
Details	binding site for residue MG C 1102

Chain	Residue
C	ASP506
C	GLU509
C	LYS528
C	POP1103

site_id	AC6
Number of Residues	10
Details	binding site for residue POP C 1103

Chain	Residue
C	ARG57
C	ASP506
C	ASN512
C	ARG515
C	GLN516
C	LYS528
C	ASP576
C	MG1101
C	MG1102
D	GLY76

Functional Information from PROSITE/UniProt

site_id	PS00299
Number of Residues	26
Details	UBIQUITIN_1 Ubiquitin domain signature. KakIqDkegIPpdqQrLIFaGkqleD

Chain	Residue	Details
B	LYS27-ASP52

site_id	PS00536
Number of Residues	9
Details	UBIQUITIN_ACTIVAT_1 Ubiquitin-activating enzyme signature 1. KACSGKFmP

Chain	Residue	Details
A	LYS411-PRO419

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	272
Details	Repeat: {"description":"1-1"}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	304
Details	Repeat: {"description":"1-2"}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	1096
Details	Region: {"description":"2 approximate repeats"}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	2
Details	Active site: {"description":"Glycyl thioester intermediate","evidences":[{"source":"PROSITE-ProRule","id":"PRU10132","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	10
Details	Binding site: {"evidences":[{"source":"UniProtKB","id":"P22515","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	2
Details	Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"Q02053","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	2
Details	Modified residue: {"description":"N6-succinyllysine","evidences":[{"source":"UniProtKB","id":"Q02053","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	4
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	2
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"18669648","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18669648","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"Q02053","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI12
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"24275569","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI13
Number of Residues	150
Details	Domain: {"description":"Ubiquitin-like","evidences":[{"source":"PROSITE-ProRule","id":"PRU00214","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI14
Number of Residues	4
Details	Site: {"description":"Interacts with activating enzyme"}

Chain

Residue

Details

site_id	SWS_FT_FI15
Number of Residues	2
Details	Site: {"description":"Essential for function"}

Chain

Residue

Details

site_id	SWS_FT_FI16
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine; by PINK1","evidences":[{"source":"PubMed","id":"24660806","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"24751536","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"24784582","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"25527291","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI17
Number of Residues	2
Details	Modified residue: {"description":"(Microbial infection) ADP-ribosylthreonine","evidences":[{"source":"PubMed","id":"32330457","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI18
Number of Residues	2
Details	Modified residue: {"description":"ADP-ribosylglycine","evidences":[{"source":"PubMed","id":"28525742","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI19
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"16443603","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI20
Number of Residues	4
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)"}

Chain

Residue

Details

site_id	SWS_FT_FI21
Number of Residues	4
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"16443603","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16543144","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI22
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"15466860","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI23
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"16543144","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"25752573","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"25752577","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"34239127","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI24
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"25752577","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI25
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"16543144","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18719106","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)