5TR4

Structure of Ubiquitin activating enzyme (Uba1) in complex with ubiquitin and TAK-243

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	21
Details	binding site for residue 61T B 101

Chain	Residue
A	GLY443
A	VAL520
A	PRO522
A	ALA542
A	LEU543
A	ASP544
A	ASN545
A	ASP547
A	ALA548
A	TYR551
A	HOH1201
A	ALA444
A	HOH1300
B	GLY76
A	ASP470
A	MET471
A	ASP472
A	ARG481
A	GLN482
A	LYS494
A	ARG519

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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

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Functional Information from SwissProt/UniProt

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

Chain

Residue

Details

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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

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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 4","evidences":[{"source":"PROSITE-ProRule","id":"PRU00214","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

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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

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