Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5L6H

Uba1 in complex with Ub-ABPA3 covalent adduct

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide 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	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	0036211	biological_process	protein modification process
A	0046872	molecular_function	metal ion binding
C	0000166	molecular_function	nucleotide 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	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	0036211	biological_process	protein modification process
C	0046872	molecular_function	metal ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	11
Details	binding site for residue SO4 A 1101

Chain	Residue
A	ARG21
A	HOH1337
B	6O2101
A	ASN478
A	ARG481
A	HOH1214
A	HOH1217
A	HOH1239
A	HOH1286
A	HOH1287
A	HOH1300

site_id	AC2
Number of Residues	2
Details	binding site for residue CL A 1102

Chain	Residue
A	THR571
A	LYS572

site_id	AC3
Number of Residues	2
Details	binding site for residue CL A 1103

Chain	Residue
A	ARG861
B	ARG74

site_id	AC4
Number of Residues	1
Details	binding site for residue CL A 1104

Chain	Residue
A	ARG96

site_id	AC5
Number of Residues	1
Details	binding site for residue CL A 1105

Chain	Residue
A	VAL117

site_id	AC6
Number of Residues	10
Details	binding site for residue GOL A 1106

Chain	Residue
A	ASP282
A	LYS285
A	PHE391
A	ASP392
A	SER393
A	GLU395
A	PHE908
A	HOH1255
A	HOH1259
A	HOH1363

site_id	AC7
Number of Residues	4
Details	binding site for residue GOL A 1107

Chain	Residue
A	ARG288
A	ASN344
A	LEU394
A	HOH1203

site_id	AC8
Number of Residues	5
Details	binding site for residue GOL A 1108

Chain	Residue
A	LYS137
A	SER153
A	GLU155
A	ASN162
A	HOH1318

site_id	AC9
Number of Residues	3
Details	binding site for residue GOL A 1109

Chain	Residue
A	LEU811
A	GLY813
A	PHE814

site_id	AD1
Number of Residues	4
Details	binding site for residue GOL A 1110

Chain	Residue
A	VAL819
A	ASN828
A	HIS830
A	HOH1395

site_id	AD2
Number of Residues	1
Details	binding site for residue GOL A 1111

Chain	Residue
A	ARG713

site_id	AD3
Number of Residues	3
Details	binding site for residue GOL A 1112

Chain	Residue
A	TYR24
A	LYS854
A	HOH1333

site_id	AD4
Number of Residues	18
Details	binding site for residue 6O2 B 101

Chain	Residue
A	GLY443
A	ALA444
A	ASP470
A	ASP472
A	ARG481
A	GLN482
A	LYS494
A	VAL520
A	ALA542
A	LEU543
A	ASP544
A	ASN545
A	ALA548
A	SO41101
A	HOH1239
B	GLY76
B	HOH214
B	HOH220

site_id	AD5
Number of Residues	11
Details	binding site for residue SO4 C 1101

Chain	Residue
C	ARG21
C	ASN478
C	ARG481
C	HOH1245
C	HOH1274
C	HOH1278
C	HOH1288
C	HOH1306
C	HOH1367
C	HOH1443
D	6O2101

site_id	AD6
Number of Residues	2
Details	binding site for residue CL C 1102

Chain	Residue
C	THR571
C	HOH1442

site_id	AD7
Number of Residues	1
Details	binding site for residue CL C 1103

Chain	Residue
C	ASN514

site_id	AD8
Number of Residues	2
Details	binding site for residue CL C 1104

Chain	Residue
C	ARG861
D	ARG74

site_id	AD9
Number of Residues	7
Details	binding site for residue MG C 1106

Chain	Residue
A	GLU944
A	HOH1207
A	HOH1418
A	HOH1423
C	ASP1008
C	HOH1214
C	HOH1269

site_id	AE1
Number of Residues	3
Details	binding site for residue GOL C 1107

Chain	Residue
C	ARG713
C	ALA714
C	PHE846

site_id	AE2
Number of Residues	4
Details	binding site for residue GOL C 1108

Chain	Residue
C	LYS267
C	GLN271
C	SER274
C	ASN275

site_id	AE3
Number of Residues	11
Details	binding site for residue GOL C 1109

Chain	Residue
C	SER393
C	GLU395
C	LYS895
C	PHE908
C	HOH1223
C	HOH1315
C	HOH1354
C	ASP282
C	LYS285
C	PHE391
C	ASP392

site_id	AE4
Number of Residues	2
Details	binding site for residue GOL C 1110

Chain	Residue
C	ARG288
C	ASN344

site_id	AE5
Number of Residues	3
Details	binding site for residue ACT C 1111

Chain	Residue
C	LEU114
C	VAL117
C	ASP136

site_id	AE6
Number of Residues	19
Details	binding site for Di-peptide 6O2 D 101 and GLY D 76

Chain	Residue
C	GLY443
C	ALA444
C	ILE445
C	ASP470
C	ASN471
C	ASP472
C	ARG481
C	GLN482
C	LYS494
C	VAL520
C	ALA542
C	LEU543
C	ASP544
C	ASN545
C	ALA548
C	SO41101
C	HOH1278
C	HOH1319
D	GLY75

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

Chain	Residue	Details
A	LYS376-PRO384

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

Chain	Residue	Details
A	PRO598-PRO606

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	274
Details	Repeat: {"description":"1-1"}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	308
Details	Repeat: {"description":"1-2"}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	1104
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"},{"source":"PubMed","id":"24816100","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	14
Details	Binding site: {"evidences":[{"source":"PubMed","id":"35970836","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"7ZH9","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	10
Details	Binding site: {"evidences":[{"source":"PubMed","id":"35970836","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"24816100","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"7ZH9","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"17287358","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18407956","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	6
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"22106047","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
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_FI11
Number of Residues	22
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"UniProtKB","id":"P62979","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI12
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

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	8
Details	M-CSA 307

Chain	Residue	Details
A	ARG21	electrostatic stabiliser, hydrogen bond donor, steric role
A	ARG481	electrostatic stabiliser, hydrogen bond donor, steric role
A	ASP544	steric role
A	CYS600	activator, covalently attached, hydrogen bond donor, nucleophile, proton donor
A	THR601	hydrogen bond acceptor, hydrogen bond donor, increase acidity, increase nucleophilicity, proton acceptor, proton donor, proton relay
A	ARG603	electrostatic stabiliser, hydrogen bond donor
A	ASN781	electrostatic stabiliser, hydrogen bond donor
A	ASP782	electrostatic stabiliser, hydrogen bond donor

site_id	MCSA2
Number of Residues	5
Details	M-CSA 939

Chain	Residue	Details
A	CYS600	nucleofuge
A	THR601	modifies pKa
A	ARG603	electrostatic stabiliser
A	ASN781	electrostatic stabiliser
A	ASP782	electrostatic stabiliser

site_id	MCSA3
Number of Residues	8
Details	M-CSA 307

Chain	Residue	Details
C	ARG21	electrostatic stabiliser, hydrogen bond donor, steric role
C	ARG481	electrostatic stabiliser, hydrogen bond donor, steric role
C	ASP544	steric role
C	CYS600	activator, covalently attached, hydrogen bond donor, nucleophile, proton donor
C	THR601	hydrogen bond acceptor, hydrogen bond donor, increase acidity, increase nucleophilicity, proton acceptor, proton donor, proton relay
C	ARG603	electrostatic stabiliser, hydrogen bond donor
C	ASN781	electrostatic stabiliser, hydrogen bond donor
C	ASP782	electrostatic stabiliser, hydrogen bond donor

site_id	MCSA4
Number of Residues	5
Details	M-CSA 939

Chain	Residue	Details
C	CYS600	nucleofuge
C	THR601	modifies pKa
C	ARG603	electrostatic stabiliser
C	ASN781	electrostatic stabiliser
C	ASP782	electrostatic stabiliser

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