Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6NYA

Crystal Structure of ubiquitin E1 (Uba1) in complex with Ubc3 (Cdc34) and ubiquitin

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
B	0003729	molecular_function	mRNA binding
B	0005634	cellular_component	nucleus
B	0005737	cellular_component	cytoplasm
D	0000166	molecular_function	nucleotide binding
D	0004839	molecular_function	ubiquitin activating enzyme activity
D	0005515	molecular_function	protein binding
D	0005524	molecular_function	ATP binding
D	0005634	cellular_component	nucleus
D	0005737	cellular_component	cytoplasm
D	0006511	biological_process	ubiquitin-dependent protein catabolic process
D	0006974	biological_process	DNA damage response
D	0008641	molecular_function	ubiquitin-like modifier activating enzyme activity
D	0016567	biological_process	protein ubiquitination
D	0016874	molecular_function	ligase activity
D	0036211	biological_process	protein modification process
D	0046872	molecular_function	metal ion binding
E	0003729	molecular_function	mRNA binding
E	0005634	cellular_component	nucleus
E	0005737	cellular_component	cytoplasm

Functional Information from PDB Data

site_id	AC1
Number of Residues	29
Details	binding site for residue ATP A 1101

Chain	Residue
A	ARG21
A	LYS519
A	VAL520
A	ALA542
A	LEU543
A	ASP544
A	ASN545
A	ALA548
A	MG1102
A	HOH1268
A	HOH1271
A	GLY443
A	HOH1275
A	HOH1299
A	HOH1372
A	HOH1381
A	HOH1398
A	HOH1407
A	HOH1467
A	HOH1473
A	HOH1544
B	GLY76
A	ALA444
A	ASP470
A	ASP472
A	ASN478
A	ARG481
A	GLN482
A	LYS494

site_id	AC2
Number of Residues	4
Details	binding site for residue MG A 1102

Chain	Residue
A	ASP544
A	ATP1101
A	HOH1381
A	HOH1467

site_id	AC3
Number of Residues	4
Details	binding site for residue SO4 A 1103

Chain	Residue
A	GLU217
A	GLY218
A	LEU219
A	ASP220

site_id	AC4
Number of Residues	3
Details	binding site for residue SO4 A 1104

Chain	Residue
A	ASN38
A	SER62
A	GLN122

site_id	AC5
Number of Residues	4
Details	binding site for residue SO4 A 1106

Chain	Residue
A	ARG554
A	ILE1002
A	PHE1019
A	HOH1338

site_id	AC6
Number of Residues	3
Details	binding site for residue SO4 A 1107

Chain	Residue
A	TYR465
A	VAL467
A	ASN514

site_id	AC7
Number of Residues	3
Details	binding site for residue SO4 A 1108

Chain	Residue
A	ASP851
A	ARG852
A	GLN853

site_id	AC8
Number of Residues	5
Details	binding site for residue SO4 A 1109

Chain	Residue
A	GLY27
A	LYS28
A	GLU29
A	HOH1291
A	HOH1458

site_id	AC9
Number of Residues	2
Details	binding site for residue SO4 A 1110

Chain	Residue
A	ARG288
A	ASN344

site_id	AD1
Number of Residues	4
Details	binding site for residue EDO A 1111

Chain	Residue
A	ASN545
A	VAL546
A	ASP547
B	ARG74

site_id	AD2
Number of Residues	3
Details	binding site for residue EDO A 1112

Chain	Residue
A	ARG96
A	ALA97
A	HOH1379

site_id	AD3
Number of Residues	8
Details	binding site for residue EDO A 1113

Chain	Residue
A	ASP282
A	LYS285
A	ASP392
A	GLU395
A	LYS895
A	PHE908
A	HOH1321
A	HOH1351

site_id	AD4
Number of Residues	5
Details	binding site for residue EDO A 1114

Chain	Residue
A	ILE254
A	ASN607
A	PHE846
A	ILE847
A	GLU848

site_id	AD5
Number of Residues	7
Details	binding site for residue EDO A 1115

Chain	Residue
A	SER146
A	SER147
A	GLY148
A	HOH1262
D	THR849
D	ALA850
D	ASP851

site_id	AD6
Number of Residues	6
Details	binding site for residue EDO A 1116

Chain	Residue
A	GLU534
A	PHE558
A	TYR559
A	HIS1023
A	HOH1296
A	HOH1508

site_id	AD7
Number of Residues	3
Details	binding site for residue EDO A 1117

Chain	Residue
A	GLU155
A	PHE296
A	HIS300

site_id	AD8
Number of Residues	6
Details	binding site for residue EDO A 1118

Chain	Residue
A	GLU13
A	ILE14
A	ASP15
A	TYR19
A	GLN35
A	TYR105

site_id	AD9
Number of Residues	3
Details	binding site for residue EDO A 1119

Chain	Residue
A	TYR919
A	ARG930
A	HOH1547

site_id	AE1
Number of Residues	4
Details	binding site for residue EDO A 1120

Chain	Residue
A	PHE821
A	GLU822
A	LYS823
A	GLY860

site_id	AE2
Number of Residues	3
Details	binding site for residue EDO A 1121

Chain	Residue
A	ASN434
A	GLY461
A	SER462

site_id	AE3
Number of Residues	4
Details	binding site for residue EDO C 201

Chain	Residue
C	GLN76
C	PHE77
C	ARG93
C	LEU94

site_id	AE4
Number of Residues	4
Details	binding site for residue MG D 1201

Chain	Residue
D	ASP544
D	ATP1202
D	HOH1437
D	HOH1504

site_id	AE5
Number of Residues	29
Details	binding site for residue ATP D 1202

Chain	Residue
D	ARG21
D	GLY443
D	ALA444
D	ASP470
D	ASP472
D	ASN478
D	ARG481
D	GLN482
D	LYS494
D	LYS519
D	VAL520
D	ALA542
D	LEU543
D	ASP544
D	ASN545
D	ALA548
D	MG1201
D	HOH1333
D	HOH1341
D	HOH1366
D	HOH1368
D	HOH1381
D	HOH1390
D	HOH1437
D	HOH1456
D	HOH1465
D	HOH1504
D	HOH1507
E	GLY76

site_id	AE6
Number of Residues	2
Details	binding site for residue SO4 D 1203

Chain	Residue
D	LEU114
D	VAL117

site_id	AE7
Number of Residues	7
Details	binding site for residue SO4 D 1204

Chain	Residue
D	VAL557
D	PHE558
D	ARG560
D	TRP928
D	ASP929
D	ARG930
D	PHE1019

site_id	AE8
Number of Residues	6
Details	binding site for residue SO4 D 1205

Chain	Residue
D	GLY27
D	LYS28
D	GLU29
D	EDO1211
D	HOH1306
D	HOH1511

site_id	AE9
Number of Residues	5
Details	binding site for residue SO4 D 1206

Chain	Residue
D	GLU217
D	GLY218
D	LEU219
D	ASP220
D	HOH1578

site_id	AF1
Number of Residues	2
Details	binding site for residue SO4 D 1207

Chain	Residue
D	ARG288
D	ASN344

site_id	AF2
Number of Residues	3
Details	binding site for residue SO4 D 1208

Chain	Residue
D	ASP851
D	ARG852
D	GLN853

site_id	AF3
Number of Residues	2
Details	binding site for residue SO4 D 1209

Chain	Residue
D	ARG305
D	LYS324

site_id	AF4
Number of Residues	4
Details	binding site for residue EDO D 1210

Chain	Residue
D	ASN545
D	VAL546
D	ASP547
E	ARG74

site_id	AF5
Number of Residues	6
Details	binding site for residue EDO D 1211

Chain	Residue
D	TYR24
D	VAL25
D	GLY27
D	GLY178
D	LYS381
D	SO41205

site_id	AF6
Number of Residues	4
Details	binding site for residue EDO D 1212

Chain	Residue
D	ILE14
D	ASP15
D	GLU16
D	SER17

site_id	AF7
Number of Residues	5
Details	binding site for residue EDO D 1213

Chain	Residue
D	GLU13
D	ILE14
D	ASP15
D	TYR19
D	GLN35

site_id	AF8
Number of Residues	3
Details	binding site for residue EDO D 1214

Chain	Residue
D	ARG554
D	VAL557
D	PHE1019

site_id	AF9
Number of Residues	6
Details	binding site for residue EDO D 1215

Chain	Residue
D	ASN38
D	SER62
D	ASN109
D	GLN122
D	PHE123
D	HOH1537

site_id	AG1
Number of Residues	2
Details	binding site for residue EDO D 1216

Chain	Residue
D	ARG150
D	THR172

site_id	AG2
Number of Residues	5
Details	binding site for residue EDO D 1217

Chain	Residue
D	GLU155
D	PHE296
D	GLN297
D	HIS300
D	HOH1358

site_id	AG3
Number of Residues	3
Details	binding site for residue EDO D 1218

Chain	Residue
D	ARG312
D	GLU317
D	HOH1478

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
C	TYR84-LEU99

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	2
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_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

site_id	SWS_FT_FI13
Number of Residues	2
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

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	6
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

site_id	MCSA2
Number of Residues	3
Details	M-CSA 939

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

site_id	MCSA3
Number of Residues	6
Details	M-CSA 307

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

site_id	MCSA4
Number of Residues	3
Details	M-CSA 939

Chain	Residue	Details
D	CYS600	nucleofuge
D	THR601	modifies pKa
D	ARG603	electrostatic stabiliser

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