Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4II3

Crystal structure of S. pombe Ubiquitin activating enzyme 1 (Uba1) in complex with 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	0000287	molecular_function	magnesium ion 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	0005737	cellular_component	cytoplasm
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	0016567	biological_process	protein ubiquitination
C	0016874	molecular_function	ligase activity
C	0016887	molecular_function	ATP hydrolysis activity
C	0036211	biological_process	protein modification process
C	0046872	molecular_function	metal ion binding

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	HOH1226
A	HOH1263

site_id	AC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MG A 1102

Chain	Residue
A	ASP465
A	GLU468
A	ATP1103

site_id	AC3
Number of Residues	20
Details	BINDING SITE FOR RESIDUE ATP A 1103

Chain	Residue
A	ALA437
A	ASP463
A	MET464
A	ASP465
A	ARG474
A	LYS487
A	VAL513
A	ALA535
A	ASP537
A	ASN538
A	ALA541
A	MG1101
A	MG1102
A	HOH1226
A	HOH1246
A	HOH1259
A	HOH1263
B	GLY76
A	ARG22
A	GLY436

site_id	AC4
Number of Residues	2
Details	BINDING SITE FOR RESIDUE CA A 1104

Chain	Residue
A	ASP918
A	HOH1202

site_id	AC5
Number of Residues	2
Details	BINDING SITE FOR RESIDUE CA A 1105

Chain	Residue
A	GLU205
A	HOH1230

site_id	AC6
Number of Residues	1
Details	BINDING SITE FOR RESIDUE CA A 1106

Chain	Residue
A	GLU665

site_id	AC7
Number of Residues	2
Details	BINDING SITE FOR RESIDUE CA A 1107

Chain	Residue
A	TYR920
A	GLU938

site_id	AC8
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MG C 1101

Chain	Residue
C	ASP537
C	ATP1103
C	HOH1213

site_id	AC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MG C 1102

Chain	Residue
C	ASP465
C	GLU468
C	ATP1103

site_id	BC1
Number of Residues	18
Details	BINDING SITE FOR RESIDUE ATP C 1103

Chain	Residue
C	ARG22
C	GLY436
C	ALA437
C	ASP463
C	MET464
C	ASP465
C	ASN471
C	ARG474
C	LYS487
C	ARG512
C	VAL513
C	ALA535
C	ASP537
C	ASN538
C	MG1101
C	MG1102
C	HOH1213
D	GLY76

site_id	BC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CA C 1104

Chain	Residue
A	THR261
C	ASP996
C	GLY1000
C	HOH1240

site_id	BC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE CA C 1105

Chain	Residue
C	ASP918
C	HOH1241
C	HOH1242

site_id	BC4
Number of Residues	2
Details	BINDING SITE FOR RESIDUE CA C 1106

Chain	Residue
C	ASP611
C	GLN619

site_id	BC5
Number of Residues	1
Details	BINDING SITE FOR RESIDUE CA C 1107

Chain	Residue
C	GLU938

site_id	BC6
Number of Residues	1
Details	BINDING SITE FOR RESIDUE CA C 1108

Chain	Residue
C	TYR920

site_id	BC7
Number of Residues	1
Details	BINDING SITE FOR RESIDUE CA C 1109

Chain	Residue
C	THR657

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
B	LYS27-ASP52

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	2
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	12
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	8
Details	Binding site: {"evidences":[{"source":"UniProtKB","id":"P22515","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	2
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	4
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"P22515","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	4
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	150
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	8
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	4
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	6
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

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