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1Y8Q
Asym. Unit
Info
Asym.Unit (288 KB)
Biol.Unit 1 (144 KB)
Biol.Unit 2 (141 KB)
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(1)
Title
:
SUMO E1 ACTIVATING ENZYME SAE1-SAE2-MG-ATP COMPLEX
Authors
:
L. M. Lois, C. D. Lima
Date
:
13 Dec 04 (Deposition) - 25 Jan 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.25
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Sumo; E1; Heterodimer; Activating Enzyme; Ubl, Ligase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. M. Lois, C. D. Lima
Structures Of The Sumo E1 Provide Mechanistic Insights Into Sumo Activation And E2 Recruitment To E1
Embo J. V. 24 439 2005
(for further references see the
PDB file header
)
[
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Hetero Components
(3, 6)
Info
All Hetero Components
1a: ADENOSINE-5'-TRIPHOSPHATE (ATPa)
1b: ADENOSINE-5'-TRIPHOSPHATE (ATPb)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ATP
2
Ligand/Ion
ADENOSINE-5'-TRIPHOSPHATE
2
MG
2
Ligand/Ion
MAGNESIUM ION
3
ZN
2
Ligand/Ion
ZINC ION
[
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Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP D:117 , ATP D:801 , HOH D:851 , HOH D:903 , HOH D:991
BINDING SITE FOR RESIDUE MG D 641
2
AC2
SOFTWARE
ASP B:117 , ATP B:802 , HOH B:935 , HOH B:978 , HOH B:1065
BINDING SITE FOR RESIDUE MG B 641
3
AC3
SOFTWARE
CYS D:158 , CYS D:161 , CYS D:441 , CYS D:444
BINDING SITE FOR RESIDUE ZN D 642
4
AC4
SOFTWARE
CYS B:158 , CYS B:161 , CYS B:441 , CYS B:444
BINDING SITE FOR RESIDUE ZN B 642
5
AC5
SOFTWARE
ARG C:21 , GLY D:26 , GLY D:27 , ASP D:48 , LEU D:49 , ASP D:50 , ASN D:56 , ARG D:59 , GLN D:60 , LYS D:72 , ASP D:94 , SER D:95 , ILE D:96 , LEU D:116 , ASP D:117 , LYS D:346 , MG D:641 , HOH D:837 , HOH D:842 , HOH D:851 , HOH D:866 , HOH D:903 , HOH D:908 , HOH D:991
BINDING SITE FOR RESIDUE ATP D 801
6
AC6
SOFTWARE
ARG A:21 , GLY B:26 , GLY B:27 , ASP B:48 , LEU B:49 , ASP B:50 , ASN B:56 , ARG B:59 , GLN B:60 , LYS B:72 , ASP B:94 , SER B:95 , ILE B:96 , MET B:97 , LEU B:116 , ASP B:117 , ASN B:118 , ALA B:121 , LYS B:346 , MG B:641 , HOH B:818 , HOH B:829 , HOH B:839 , HOH B:875 , HOH B:879 , HOH B:918 , HOH B:935 , HOH B:978 , HOH B:1065
BINDING SITE FOR RESIDUE ATP B 802
[
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SAPs(SNPs)/Variants
(1, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_017689 (L307R, chain B/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_017689
L
307
R
SAE2_HUMAN
Polymorphism
1043062
B/D
L
307
R
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: UBIQUITIN_ACTIVAT_2 (B:171-179,D:171-179)
2: UBIQUITIN_ACTIVAT_1 (B:404-412,D:404-412)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
UBIQUITIN_ACTIVAT_2
PS00865
Ubiquitin-activating enzyme active site.
SAE2_HUMAN
171-179
2
B:171-179
D:171-179
2
UBIQUITIN_ACTIVAT_1
PS00536
Ubiquitin-activating enzyme signature 1.
SAE2_HUMAN
404-412
2
B:404-412
D:404-412
[
close PROSITE info
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Exons
(25, 50)
Info
All Exons
Exon 1.1 (B:6-46 | D:4-46)
Exon 1.2 (B:47-74 | D:47-74)
Exon 1.3 (B:75-98 | D:75-98)
Exon 1.4 (B:98-120 | D:98-120)
Exon 1.5 (B:120-153 | D:120-153)
Exon 1.6 (B:154-194 | D:154-194)
Exon 1.7 (B:194-217 | D:194-217)
Exon 1.8 (B:217-257 (gaps) | D:217-257 (gaps...)
Exon 1.9 (B:258-290 | D:258-290)
Exon 1.10 (B:305-346 | D:305-346)
Exon 1.11 (B:347-378 | D:347-378)
Exon 1.12 (B:378-415 | D:378-415)
Exon 1.13 (B:416-467 | D:416-467)
Exon 1.14 (B:468-500 | D:468-500)
Exon 1.15 (B:500-535 | D:500-535)
Exon 1.16 (B:535-550 | D:535-550)
Exon 2.1b (A:10-33 | C:9-33)
Exon 2.2 (A:33-70 | C:33-70)
Exon 2.3 (A:71-128 | C:71-128)
Exon 2.4 (A:129-176 | C:129-176)
Exon 2.5 (A:176-209 (gaps) | C:176-209 (gaps...)
Exon 2.6 (A:210-245 | C:210-245)
Exon 2.8 (A:245-293 | C:245-293)
Exon 2.9 (A:293-316 | C:293-316)
Exon 2.10b (A:317-345 | C:317-345)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1
02: Boundary 1.1/1.2
03: Boundary 1.2/1.3
04: Boundary 1.3/1.4
05: Boundary 1.4/1.5
06: Boundary 1.5/1.6
07: Boundary 1.6/1.7
08: Boundary 1.7/1.8
09: Boundary 1.8/1.9
10: Boundary 1.9/1.10
11: Boundary 1.10/1.11
12: Boundary 1.11/1.12
13: Boundary 1.12/1.13
14: Boundary 1.13/1.14
15: Boundary 1.14/1.15
16: Boundary 1.15/1.16
17: Boundary 1.16/1.17
18: Boundary -/2.1b
19: Boundary 2.1b/2.2
20: Boundary 2.2/2.3
21: Boundary 2.3/2.4
22: Boundary 2.4/2.5
23: Boundary 2.5/2.6
24: Boundary 2.6/2.8
25: Boundary 2.8/2.9
26: Boundary 2.9/2.10b
27: Boundary 2.10b/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1
ENST00000246548
1
ENSE00000862687
chr19:
34919268-34919475
208
SAE2_HUMAN
1-46
46
2
B:6-46
D:4-46
41
43
1.2
ENST00000246548
2
ENSE00000862688
chr19:
34921481-34921564
84
SAE2_HUMAN
47-74
28
2
B:47-74
D:47-74
28
28
1.3
ENST00000246548
3
ENSE00000862689
chr19:
34922766-34922836
71
SAE2_HUMAN
75-98
24
2
B:75-98
D:75-98
24
24
1.4
ENST00000246548
4
ENSE00000862690
chr19:
34924253-34924317
65
SAE2_HUMAN
98-120
23
2
B:98-120
D:98-120
23
23
1.5
ENST00000246548
5
ENSE00000862691
chr19:
34925773-34925873
101
SAE2_HUMAN
120-153
34
2
B:120-153
D:120-153
34
34
1.6
ENST00000246548
6
ENSE00000862692
chr19:
34929550-34929671
122
SAE2_HUMAN
154-194
41
2
B:154-194
D:154-194
41
41
1.7
ENST00000246548
7
ENSE00000862693
chr19:
34934749-34934816
68
SAE2_HUMAN
194-217
24
2
B:194-217
D:194-217
24
24
1.8
ENST00000246548
8
ENSE00000862694
chr19:
34935905-34936026
122
SAE2_HUMAN
217-257
41
2
B:217-257 (gaps)
D:217-257 (gaps)
41
41
1.9
ENST00000246548
9
ENSE00000862695
chr19:
34941170-34941269
100
SAE2_HUMAN
258-291
34
2
B:258-290
D:258-290
33
33
1.10
ENST00000246548
10
ENSE00000862696
chr19:
34942886-34943052
167
SAE2_HUMAN
291-346
56
2
B:305-346
D:305-346
42
42
1.11
ENST00000246548
11
ENSE00000862697
chr19:
34945165-34945258
94
SAE2_HUMAN
347-378
32
2
B:347-378
D:347-378
32
32
1.12
ENST00000246548
12
ENSE00000862698
chr19:
34945349-34945461
113
SAE2_HUMAN
378-415
38
2
B:378-415
D:378-415
38
38
1.13
ENST00000246548
13
ENSE00000862699
chr19:
34949674-34949829
156
SAE2_HUMAN
416-467
52
2
B:416-467
D:416-467
52
52
1.14
ENST00000246548
14
ENSE00000862700
chr19:
34951375-34951471
97
SAE2_HUMAN
468-500
33
2
B:468-500
D:468-500
33
33
1.15
ENST00000246548
15
ENSE00000862701
chr19:
34954931-34955036
106
SAE2_HUMAN
500-535
36
2
B:500-535
D:500-535
36
36
1.16
ENST00000246548
16
ENSE00000862702
chr19:
34957783-34957919
137
SAE2_HUMAN
535-581
47
2
B:535-550
D:535-550
16
16
1.17
ENST00000246548
17
ENSE00000862703
chr19:
34959945-34960795
851
SAE2_HUMAN
581-640
60
0
-
-
2.1b
ENST00000270225
1b
ENSE00001602790
chr19:
47634144-47634285
142
SAE1_HUMAN
1-33
33
2
A:10-33
C:9-33
24
25
2.2
ENST00000270225
2
ENSE00000953004
chr19:
47646751-47646862
112
SAE1_HUMAN
33-70
38
2
A:33-70
C:33-70
38
38
2.3
ENST00000270225
3
ENSE00000953005
chr19:
47653459-47653632
174
SAE1_HUMAN
71-128
58
2
A:71-128
C:71-128
58
58
2.4
ENST00000270225
4
ENSE00000953006
chr19:
47656155-47656297
143
SAE1_HUMAN
129-176
48
2
A:129-176
C:129-176
48
48
2.5
ENST00000270225
5
ENSE00000953007
chr19:
47658371-47658470
100
SAE1_HUMAN
176-209
34
2
A:176-209 (gaps)
C:176-209 (gaps)
34
34
2.6
ENST00000270225
6
ENSE00000953008
chr19:
47673075-47673180
106
SAE1_HUMAN
210-245
36
2
A:210-245
C:210-245
36
36
2.8
ENST00000270225
8
ENSE00001698339
chr19:
47700490-47700634
145
SAE1_HUMAN
245-293
49
2
A:245-293
C:245-293
49
49
2.9
ENST00000270225
9
ENSE00001799877
chr19:
47706928-47706997
70
SAE1_HUMAN
293-316
24
2
A:293-316
C:293-316
24
24
2.10b
ENST00000270225
10b
ENSE00001604339
chr19:
47712416-47713532
1117
SAE1_HUMAN
317-346
30
2
A:317-345
C:317-345
29
29
[
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SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
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CATH Domains
(3, 8)
Info
all CATH domains
1a: CATH_1y8qB01 (B:6-166,B:386-446)
1b: CATH_1y8qD01 (D:4-167,D:383-445)
1c: CATH_1y8qC00 (C:9-345)
1d: CATH_1y8qA00 (A:10-345)
2a: CATH_1y8qD03 (D:446-550)
2b: CATH_1y8qB03 (B:447-550)
3a: CATH_1y8qD02 (D:168-382)
3b: CATH_1y8qB02 (B:167-385)
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)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Human (Homo sapiens)
(188)
1a
1y8qB01
B:6-166,B:386-446
1b
1y8qD01
D:4-167,D:383-445
1c
1y8qC00
C:9-345
1d
1y8qA00
A:10-345
Architecture
:
Roll
(3276)
Topology
:
Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A
(114)
Homologous Superfamily
:
Ubiquitin-like 2 activating enzyme e1b. Chain: B, domain 3
(2)
Human (Homo sapiens)
(2)
2a
1y8qD03
D:446-550
2b
1y8qB03
B:447-550
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Ubiquitin-like 1 activating enzyme e1a, chain B, domain 2
(2)
Homologous Superfamily
:
Ubiquitin-like 1 activating enzyme e1a, chain B, domain 2
(2)
Human (Homo sapiens)
(2)
3a
1y8qD02
D:168-382
3b
1y8qB02
B:167-385
[
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Pfam Domains
(3, 8)
Info
all PFAM domains
1a: PFAM_ThiF_1y8qC01 (C:35-168)
1b: PFAM_ThiF_1y8qC02 (C:35-168)
1c: PFAM_ThiF_1y8qD01 (D:16-151)
1d: PFAM_ThiF_1y8qD02 (D:16-151)
2a: PFAM_UBACT_1y8qD03 (D:343-409)
2b: PFAM_UBACT_1y8qD04 (D:343-409)
3a: PFAM_UBA_e1_thiolCys_1y8qD05 (D:154-198)
3b: PFAM_UBA_e1_thiolCys_1y8qD06 (D:154-198)
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Clan
:
NADP_Rossmann
(1239)
Family
:
ThiF
(14)
Homo sapiens (Human)
(8)
1a
ThiF-1y8qC01
C:35-168
1b
ThiF-1y8qC02
C:35-168
1c
ThiF-1y8qD01
D:16-151
1d
ThiF-1y8qD02
D:16-151
Clan
:
no clan defined [family: UBACT]
(10)
Family
:
UBACT
(10)
Homo sapiens (Human)
(9)
2a
UBACT-1y8qD03
D:343-409
2b
UBACT-1y8qD04
D:343-409
Clan
:
no clan defined [family: UBA_e1_thiolCys]
(10)
Family
:
UBA_e1_thiolCys
(10)
Homo sapiens (Human)
(9)
3a
UBA_e1_thiolCys-1y8qD05
D:154-198
3b
UBA_e1_thiolCys-1y8qD06
D:154-198
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