6ZQH

Yeast Uba1 in complex with 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	4
Details	binding site for residue BME A 1101

Chain	Residue
A	TYR465
A	GLY511
A	ASN514
A	HOH1229

---

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

Chain	Residue
A	VAL331
A	GLN332

---

site_id	AC3
Number of Residues	8
Details	binding site for residue GOL A 1103

Chain	Residue
A	ILE863
A	HOH1206
A	HOH1299
A	HOH1451
A	HOH1593
A	ARG21
A	ARG481
A	ILE862

---

site_id	AC4
Number of Residues	4
Details	binding site for residue GOL A 1104

Chain	Residue
A	ASN402
A	HOH1219
A	HOH1255
C	ASN307

---

site_id	AC5
Number of Residues	4
Details	binding site for residue BME B 101

Chain	Residue
B	GLU51
B	ARG54
B	TYR59
B	HOH257

---

site_id	AC6
Number of Residues	13
Details	binding site for residue PG4 C 1101

Chain	Residue
C	GLU215
C	ILE254
C	ASN607
C	LYS608
C	ILE609
C	ARG713
C	PHE846
C	ILE847
C	GLU848
C	THR849
C	ALA850
C	LYS854
C	HOH1322

---

site_id	AC7
Number of Residues	5
Details	binding site for residue BME C 1102

Chain	Residue
C	TYR465
C	GLY511
C	ILE513
C	ASN514
C	HOH1201

---

site_id	AC8
Number of Residues	9
Details	binding site for residue GOL C 1103

Chain	Residue
C	PHE280
C	SER281
C	LYS285
C	ARG288
C	ALA289
C	TYR390
C	ASP392
C	HOH1398
C	HOH1607

---

site_id	AC9
Number of Residues	4
Details	binding site for residue BME D 101

Chain	Residue
D	GLU51
D	ARG54
D	HOH202
D	HOH242

---

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	14
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

---