Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4NNJ

Crystal structure of Uba1 in complex with ubiquitin-AMP and thioesterified 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
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	HOH1602
B	AMP101
A	ASN478
A	ARG481
A	ASP544
A	HOH1206
A	HOH1256
A	HOH1260
A	HOH1310
A	HOH1447

site_id	AC2
Number of Residues	9
Details	BINDING SITE FOR RESIDUE GOL A 1102

Chain	Residue
A	GLU155
A	ASN162
A	LEU273
A	HIS293
A	PHE296
A	GLN297
A	HIS300
A	TYR390
A	HOH1434

site_id	AC3
Number of Residues	10
Details	BINDING SITE FOR RESIDUE GOL A 1103

Chain	Residue
A	ASP282
A	LYS285
A	PHE391
A	ASP392
A	SER393
A	GLU395
A	PHE908
A	HOH1277
A	HOH1283
A	HOH1303

site_id	AC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE GOL A 1104

Chain	Residue
A	ARG150
A	PHE171
A	THR172

site_id	AC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE GOL A 1105

Chain	Residue
A	ASN514
A	PHE532
A	HOH1306

site_id	AC6
Number of Residues	2
Details	BINDING SITE FOR RESIDUE GOL A 1106

Chain	Residue
A	ASN344
A	HOH1649

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

Chain	Residue
A	ASN828
A	HIS830
A	HOH1344

site_id	AC8
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GOL A 1108

Chain	Residue
A	GLU534
A	PHE558
A	TYR559
A	ARG560
A	ARG930
A	ASP932
A	THR1021
A	HIS1023

site_id	AC9
Number of Residues	2
Details	BINDING SITE FOR RESIDUE GOL A 1109

Chain	Residue
A	TYR24
A	LYS854

site_id	BC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL A 1110

Chain	Residue
A	LYS349
A	GLU350
A	TYR353
A	PRO400
A	ARG405

site_id	BC2
Number of Residues	2
Details	BINDING SITE FOR RESIDUE GOL A 1111

Chain	Residue
A	HIS300
A	GLY308

site_id	BC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE GOL A 1112

Chain	Residue
A	ASP851
A	ARG852
A	GLN853

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

Chain	Residue
A	GLU29
A	LYS33
A	THR36
C	LYS33

site_id	BC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL A 1114

Chain	Residue
A	GLU500
A	CYS503
A	GLY511
A	LYS512
A	ILE513
A	HOH1590

site_id	BC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL A 1116

Chain	Residue
A	ILE1002
A	GLU1004
A	PHE1019
A	HOH1467

site_id	BC7
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL A 1117

Chain	Residue
A	LEU114
A	VAL117
A	ASP136
A	LYS139
A	HOH1432
A	HOH1437
C	TYR723

site_id	BC8
Number of Residues	2
Details	BINDING SITE FOR RESIDUE GOL A 1118

Chain	Residue
A	ASP721
C	GLU142

site_id	BC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 A 1119

Chain	Residue
A	GLY27
A	LYS28
A	GLU29

site_id	CC1
Number of Residues	19
Details	BINDING SITE FOR RESIDUE AMP B 101

Chain	Residue
A	ASN545
A	ALA548
A	SO41101
A	HOH1213
A	HOH1260
A	HOH1340
B	GLY76
A	GLY443
A	ALA444
A	ASP470
A	ASP472
A	ARG481
A	GLN482
A	LYS494
A	LYS519
A	VAL520
A	ALA542
A	LEU543
A	ASP544

site_id	CC2
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 C 1101

Chain	Residue
C	ARG21
C	ARG481
C	HOH1219
C	HOH1235
C	HOH1369
C	HOH1447
C	HOH1514
D	AMP101

site_id	CC3
Number of Residues	9
Details	BINDING SITE FOR RESIDUE GOL C 1102

Chain	Residue
C	ASP282
C	LYS285
C	ASP392
C	SER393
C	GLU395
C	PHE908
C	HOH1286
C	HOH1287
C	HOH1304

site_id	CC4
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL C 1103

Chain	Residue
C	GLU155
C	LEU273
C	HIS293
C	PHE296
C	GLN297
C	HIS300
C	TYR390

site_id	CC5
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GOL C 1104

Chain	Residue
A	SER940
A	ASP941
A	GLU944
C	THR955
C	ASP1008
C	GLY1012
C	HOH1366
C	HOH1640

site_id	CC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL C 1105

Chain	Residue
C	LEU737
C	ASN828
C	HIS830
C	HOH1313

site_id	CC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL C 1106

Chain	Residue
C	ALA284
C	ASP287
C	ARG288
C	ASN344
C	ASP346

site_id	CC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL C 1107

Chain	Residue
C	GLY27
C	GLY178
C	LYS381
C	GOL1108

site_id	CC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL C 1108

Chain	Residue
C	GLY27
C	LYS28
C	GLU29
C	GOL1107

site_id	DC1
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL C 1109

Chain	Residue
C	GLU534
C	PHE558
C	ARG560
C	ARG930
C	ASP932
C	THR1021
C	HIS1023

site_id	DC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL C 1110

Chain	Residue
C	LEU134
C	VAL138
C	LYS270
C	HOH1357
C	HOH1602

site_id	DC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE GOL C 1111

Chain	Residue
C	ASP472
C	ASP544
D	AMP101

site_id	DC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL C 1112

Chain	Residue
A	TYR723
C	LEU114
C	VAL117
C	ASP136
C	HOH1322

site_id	DC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE GOL C 1113

Chain	Residue
C	ARG150
C	PHE171
C	THR172

site_id	DC6
Number of Residues	2
Details	BINDING SITE FOR RESIDUE SO4 C 1114

Chain	Residue
C	ARG202
E	ARG42

site_id	DC7
Number of Residues	22
Details	BINDING SITE FOR RESIDUE AMP D 101

Chain	Residue
C	GLY443
C	ALA444
C	ASP470
C	ASP472
C	ARG481
C	GLN482
C	LYS494
C	LYS519
C	VAL520
C	ALA542
C	LEU543
C	ASP544
C	ASN545
C	ALA548
C	SO41101
C	GOL1111
C	HOH1201
C	HOH1216
C	HOH1273
C	HOH1369
C	HOH1447
D	GLY76

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	225
Details	Domain: {"description":"Ubiquitin-like 5","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)