Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5L6I

Uba1 in complex with Ub-MLN4924 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	8
Details	binding site for residue SO4 A 1101

Chain	Residue
A	ARG21
A	ASN478
A	ARG481
A	HOH1216
A	HOH1225
A	HOH1252
A	HOH1277
B	B39101

site_id	AC2
Number of Residues	1
Details	binding site for residue CL A 1102

Chain	Residue
A	ARG96

site_id	AC3
Number of Residues	1
Details	binding site for residue CL A 1105

Chain	Residue
A	HOH1377

site_id	AC4
Number of Residues	9
Details	binding site for residue GOL A 1109

Chain	Residue
A	ASP282
A	LYS285
A	PHE391
A	ASP392
A	SER393
A	GLU395
A	LYS895
A	HOH1229
A	HOH1288

site_id	AC5
Number of Residues	4
Details	binding site for residue GOL A 1110

Chain	Residue
A	TYR740
A	ASN828
A	HIS830
A	HOH1358

site_id	AC6
Number of Residues	7
Details	binding site for residue GOL A 1111

Chain	Residue
A	SER153
A	GLU155
A	ASN162
A	HIS293
A	PHE296
A	TYR390
A	HOH1213

site_id	AC7
Number of Residues	2
Details	binding site for residue GOL A 1112

Chain	Residue
A	ASN344
A	HOH1357

site_id	AC8
Number of Residues	3
Details	binding site for residue GOL A 1113

Chain	Residue
A	LEU134
A	GLU135
A	HOH1204

site_id	AC9
Number of Residues	4
Details	binding site for residue GOL A 1114

Chain	Residue
A	LEU114
A	VAL117
A	ASP136
A	LYS139

site_id	AD1
Number of Residues	3
Details	binding site for residue GOL A 1115

Chain	Residue
A	THR172
A	CYS378
A	SER379

site_id	AD2
Number of Residues	2
Details	binding site for residue GOL A 1116

Chain	Residue
A	ASP851
A	ARG852

site_id	AD3
Number of Residues	3
Details	binding site for residue GOL A 1117

Chain	Residue
A	ARG554
A	VAL557
A	GLU1004

site_id	AD4
Number of Residues	18
Details	binding site for residue B39 B 101

Chain	Residue
A	GLY441
A	GLY443
A	ALA444
A	ASP470
A	ASN471
A	ASP472
A	ARG481
A	GLN482
A	LYS494
A	LYS519
A	VAL520
A	ALA542
A	ASP544
A	ALA548
A	TYR551
A	SO41101
A	HOH1252
B	GLY76

site_id	AD5
Number of Residues	2
Details	binding site for residue CL B 102

Chain	Residue
A	HOH1375
B	ARG74

site_id	AD6
Number of Residues	6
Details	binding site for residue SO4 C 1101

Chain	Residue
C	ARG21
C	ASN478
C	ARG481
C	HOH1205
C	HOH1252
D	B39101

site_id	AD7
Number of Residues	2
Details	binding site for residue CL C 1103

Chain	Residue
C	ARG861
D	ARG74

site_id	AD8
Number of Residues	3
Details	binding site for residue CL C 1105

Chain	Residue
C	ARG202
E	ARG42
E	ARG72

site_id	AD9
Number of Residues	3
Details	binding site for residue CL C 1106

Chain	Residue
C	ARG288
C	GOL1114
C	HOH1384

site_id	AE1
Number of Residues	8
Details	binding site for residue GOL C 1110

Chain	Residue
C	ASP282
C	LYS285
C	ASP392
C	SER393
C	GLU395
C	HOH1238
C	HOH1243
C	HOH1285

site_id	AE2
Number of Residues	3
Details	binding site for residue GOL C 1111

Chain	Residue
C	ASP851
C	ARG852
C	GLN853

site_id	AE3
Number of Residues	6
Details	binding site for residue GOL C 1112

Chain	Residue
C	SER153
C	GLU155
C	ASN162
C	PHE296
C	GLN297
C	HIS300

site_id	AE4
Number of Residues	1
Details	binding site for residue GOL C 1113

Chain	Residue
C	GLU180

site_id	AE5
Number of Residues	4
Details	binding site for residue GOL C 1114

Chain	Residue
C	ARG288
C	ASN344
C	ASP346
C	CL1106

site_id	AE6
Number of Residues	5
Details	binding site for residue GOL C 1115

Chain	Residue
C	LYS33
C	ARG150
C	THR172
C	SER379
C	GLY380

site_id	AE7
Number of Residues	2
Details	binding site for residue GOL C 1116

Chain	Residue
C	ASN828
C	HIS830

site_id	AE8
Number of Residues	20
Details	binding site for Di-peptide B39 D 101 and GLY D 76

Chain	Residue
C	GLY441
C	GLY443
C	ALA444
C	ILE445
C	ASP470
C	ASN471
C	ASP472
C	ARG481
C	GLN482
C	LYS494
C	LYS519
C	VAL520
C	ALA542
C	LEU543
C	ASP544
C	ALA548
C	SO41101
C	HOH1289
D	GLY75
D	HOH202

site_id	AE9
Number of Residues	15
Details	binding site for Di-peptide GLY E 76 and CYS C 600

Chain	Residue
C	LEU73
C	ALA74
C	ASP75
C	SER77
C	THR78
C	LEU82
C	ARG416
C	PRO598
C	LEU599
C	THR601
C	LEU602
C	ARG603
C	SER604
C	PHE605
C	VAL780

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	21
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	6
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)