Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4II2

Crystal structure of Ubiquitin activating enzyme 1 (Uba1) in complex with the Ub E2 Ubc4, ubiquitin, and ATP/Mg

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0000287	molecular_function	magnesium ion 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	0005737	cellular_component	cytoplasm
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	0016567	biological_process	protein ubiquitination
A	0016874	molecular_function	ligase activity
A	0016887	molecular_function	ATP hydrolysis activity
A	0036211	biological_process	protein modification process
A	0046872	molecular_function	metal ion binding
C	0000166	molecular_function	nucleotide binding
C	0000209	biological_process	protein polyubiquitination
C	0004842	molecular_function	ubiquitin-protein transferase activity
C	0005515	molecular_function	protein binding
C	0005524	molecular_function	ATP binding
C	0005634	cellular_component	nucleus
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0006511	biological_process	ubiquitin-dependent protein catabolic process
C	0016567	biological_process	protein ubiquitination
C	0016740	molecular_function	transferase activity
C	0031146	biological_process	SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
C	0032933	biological_process	SREBP signaling pathway
C	0045842	biological_process	positive regulation of mitotic metaphase/anaphase transition
C	0061631	molecular_function	ubiquitin conjugating enzyme activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MG A 1101

Chain	Residue
A	ASP537
A	ATP1103
A	HOH1208
A	HOH1210

site_id	AC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG A 1102

Chain	Residue
A	HOH1211
A	ASP465
A	ATP1103
A	HOH1201
A	HOH1204
A	HOH1209

site_id	AC3
Number of Residues	29
Details	BINDING SITE FOR RESIDUE ATP A 1103

Chain	Residue
A	ARG22
A	GLY436
A	ALA437
A	ASP463
A	MET464
A	ASP465
A	ASN471
A	ARG474
A	GLN475
A	LYS487
A	ARG512
A	VAL513
A	ALA535
A	LEU536
A	ASP537
A	ASN538
A	ALA541
A	MG1101
A	MG1102
A	HOH1202
A	HOH1203
A	HOH1204
A	HOH1205
A	HOH1206
A	HOH1207
A	HOH1208
A	HOH1210
A	HOH1211
B	GLY76

site_id	AC4
Number of Residues	10
Details	BINDING SITE FOR RESIDUE PG0 A 1104

Chain	Residue
A	ASP281
A	LYS284
A	PHE386
A	ASP387
A	SER388
A	GLU390
A	LEU865
A	LEU868
A	PHE897
A	HOH1256

site_id	AC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 1105

Chain	Residue
A	HIS305
A	SER308
A	ARG311
A	ASP317
A	SO41112

site_id	AC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 1106

Chain	Residue
A	THR14
A	ILE15
A	ASP16
A	TYR20

site_id	AC7
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO A 1107

Chain	Residue
A	ARG547
A	EDO1108
A	HOH1487

site_id	AC8
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO A 1108

Chain	Residue
A	ARG548
A	PHE551
A	EDO1107

site_id	AC9
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO A 1109

Chain	Residue
A	LYS46
A	GLY47
A	LEU48
A	GLU130
A	SER155
A	ARG156
A	ASP353

site_id	BC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO A 1110

Chain	Residue
A	THR65
A	ASN122
A	HOH1648

site_id	BC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 A 1111

Chain	Residue
A	GLY28
A	HIS29
A	GLU30
A	HOH1261
A	HOH1618

site_id	BC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 A 1112

Chain	Residue
A	SER308
A	ARG311
A	ARG351
A	EDO1105
A	HOH1581
A	HOH1585

site_id	BC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 A 1113

Chain	Residue
A	ARG645
A	LEU787
C	ARG72
C	TYR145

site_id	BC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO B 101

Chain	Residue
A	GLN569
A	GLU577
A	HOH1227
B	ARG42
B	GLN49
B	HOH206

site_id	BC6
Number of Residues	2
Details	BINDING SITE FOR RESIDUE SO4 B 102

Chain	Residue
B	ARG29
B	ARG33

Functional Information from PROSITE/UniProt

site_id	PS00183
Number of Residues	16
Details	UBC_1 Ubiquitin-conjugating (UBC) active site signature. YHPNInsn.GsICLdiL

Chain	Residue	Details
C	TYR74-LEU89

site_id	PS00865
Number of Residues	9
Details	UBIQUITIN_ACTIVAT_2 Ubiquitin-activating enzyme active site. PICTLKnFP

Chain	Residue	Details
A	PRO591-PRO599

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	1
Details	Active site: {"description":"Glycyl thioester intermediate","evidences":[{"source":"PROSITE-ProRule","id":"PRU10132","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	6
Details	Binding site: {"evidences":[{"source":"PubMed","id":"23416107","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4II2","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4II3","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"UniProtKB","id":"P22515","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	1
Details	Binding site: {"evidences":[{"source":"PubMed","id":"23416107","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4II2","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"P22515","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"UniProtKB","id":"P22515","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	75
Details	Domain: {"description":"Ubiquitin-like","evidences":[{"source":"PROSITE-ProRule","id":"PRU00214","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	4
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)"}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)","evidences":[{"source":"PROSITE-ProRule","id":"PRU00214","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	3
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	146
Details	Domain: {"description":"UBC core","evidences":[{"source":"PROSITE-ProRule","id":"PRU00388","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI12
Number of Residues	1
Details	Active site: {"description":"Glycyl thioester intermediate","evidences":[{"source":"PROSITE-ProRule","id":"PRU00388","evidenceCode":"ECO:0000255"},{"source":"PROSITE-ProRule","id":"PRU10133","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

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