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2B3Y
Asym. Unit
Info
Asym.Unit (310 KB)
Biol.Unit 1 (152 KB)
Biol.Unit 2 (152 KB)
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(1)
Title
:
STRUCTURE OF A MONOCLINIC CRYSTAL FORM OF HUMAN CYTOSOLIC ACONITASE (IRP1)
Authors
:
J. Dupuy, J. C. Fontecilla-Camps, A. Volbeda
Date
:
22 Sep 05 (Deposition) - 10 Jan 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.85
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Irp1 Ire-Irp1 Aconitase Activity, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Dupuy, A. Volbeda, P. Carpentier, C. Darnault, J. M. Moulis, J. C. Fontecilla-Camps
Crystal Structure Of Human Iron Regulatory Protein 1 As Cytosolic Aconitase
Structure V. 14 129 2006
(for further references see the
PDB file header
)
[
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Hetero Components
(4, 8)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
1c: ACETATE ION (ACTc)
2a: FORMIC ACID (FMTa)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
4a: IRON/SULFUR CLUSTER (SF4a)
4b: IRON/SULFUR CLUSTER (SF4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
3
Ligand/Ion
ACETATE ION
2
FMT
1
Ligand/Ion
FORMIC ACID
3
GOL
2
Ligand/Ion
GLYCEROL
4
SF4
2
Ligand/Ion
IRON/SULFUR CLUSTER
[
close Hetero Component info
]
Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLN A:86 , PHE A:88 , THR A:89 , ARG A:713 , SER A:778 , ARG A:780 , HOH A:1045
BINDING SITE FOR RESIDUE ACT A 890
2
AC2
SOFTWARE
HIS B:126 , ASP B:205 , ILE B:507 , ARG B:536 , ARG B:541 , ACT B:891 , SF4 B:1000 , FMT B:1001 , HOH B:1186
BINDING SITE FOR RESIDUE ACT B 890
3
AC3
SOFTWARE
GLN B:86 , PHE B:88 , THR B:89 , ARG B:713 , SER B:778 , ARG B:780 , ACT B:890 , FMT B:1001
BINDING SITE FOR RESIDUE ACT B 891
4
AC4
SOFTWARE
ILE A:176 , ILE A:177 , HIS A:178 , HIS A:207 , SER A:436 , CYS A:437 , CYS A:503 , CYS A:506 , ILE A:507 , ASN A:535 , HOH A:1206
BINDING SITE FOR RESIDUE SF4 A 1000
5
AC5
SOFTWARE
ILE B:176 , ILE B:177 , HIS B:178 , HIS B:207 , SER B:436 , CYS B:437 , CYS B:503 , CYS B:506 , ASN B:535 , ACT B:890 , HOH B:1186
BINDING SITE FOR RESIDUE SF4 B 1000
6
AC6
SOFTWARE
SER A:350 , GLN A:351 , HOH A:1194 , HOH A:1474 , HOH A:1487
BINDING SITE FOR RESIDUE GOL A 1001
7
AC7
SOFTWARE
GLY A:508 , GLY A:540 , VAL A:542 , PRO A:544 , ASN A:685 , HOH A:1420
BINDING SITE FOR RESIDUE GOL A 1002
8
AC8
SOFTWARE
ASP B:205 , SER B:206 , ARG B:536 , SER B:778 , SER B:779 , ACT B:890 , ACT B:891
BINDING SITE FOR RESIDUE FMT B 1001
[
close Site info
]
SAPs(SNPs)/Variants
(3, 6)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_069413 (T318M, chain A/B, )
2: VAR_048180 (A395D, chain A/B, )
3: VAR_048181 (G486R, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_069413
T
318
M
ACOC_HUMAN
Polymorphism
---
A/B
T
318
M
2
UniProt
VAR_048180
A
395
D
ACOC_HUMAN
Polymorphism
3814519
A/B
A
395
D
3
UniProt
VAR_048181
G
486
R
ACOC_HUMAN
Polymorphism
34630459
A/B
G
486
R
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: ACONITASE_1 (A:429-445,B:429-445)
2: ACONITASE_2 (A:495-508,B:495-508)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ACONITASE_1
PS00450
Aconitase family signature 1.
ACOC_HUMAN
429-445
2
A:429-445
B:429-445
2
ACONITASE_2
PS01244
Aconitase family signature 2.
ACOC_HUMAN
495-508
2
A:495-508
B:495-508
[
close PROSITE info
]
Exons
(20, 40)
Info
All Exons
Exon 1.3 (A:2-33 | B:2-33)
Exon 1.4 (A:33-89 | B:33-89)
Exon 1.5 (A:89-135 | B:89-135)
Exon 1.6 (A:135-158 | B:135-158)
Exon 1.7 (A:159-220 | B:159-220)
Exon 1.8 (A:220-266 | B:220-266)
Exon 1.9 (A:267-324 | B:267-324)
Exon 1.10 (A:324-357 | B:324-357)
Exon 1.11 (A:358-396 | B:358-396)
Exon 1.12b (A:397-450 | B:397-450)
Exon 1.13 (A:450-495 | B:450-495)
Exon 1.14 (A:495-523 | B:495-523)
Exon 1.15 (A:524-576 | B:524-576)
Exon 1.16 (A:576-617 | B:576-617)
Exon 1.17 (A:618-652 | B:618-652)
Exon 1.18 (A:653-700 | B:653-700)
Exon 1.20 (A:700-749 | B:700-749)
Exon 1.21 (A:750-790 | B:750-790)
Exon 1.22 (A:791-852 | B:791-852)
Exon 1.23a (A:853-889 | B:853-889)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.2/1.3
02: Boundary 1.3/1.4
03: Boundary 1.4/1.5
04: Boundary 1.5/1.6
05: Boundary 1.6/1.7
06: Boundary 1.7/1.8
07: Boundary 1.8/1.9
08: Boundary 1.9/1.10
09: Boundary 1.10/1.11
10: Boundary 1.11/1.12b
11: Boundary 1.12b/1.13
12: Boundary 1.13/1.14
13: Boundary 1.14/1.15
14: Boundary 1.15/1.16
15: Boundary 1.16/1.17
16: Boundary 1.17/1.18
17: Boundary 1.18/1.20
18: Boundary 1.20/1.21
19: Boundary 1.21/1.22
20: Boundary 1.22/1.23a
21: Boundary 1.23a/-
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
1.1b
ENST00000379923
1b
ENSE00001412417
chr9:
32384618-32384733
116
ACOC_HUMAN
-
0
0
-
-
1.2
ENST00000379923
2
ENSE00001413029
chr9:
32386369-32386436
68
ACOC_HUMAN
-
0
0
-
-
1.3
ENST00000379923
3
ENSE00001606614
chr9:
32405483-32405601
119
ACOC_HUMAN
1-33
33
2
A:2-33
B:2-33
32
32
1.4
ENST00000379923
4
ENSE00000832722
chr9:
32407259-32407427
169
ACOC_HUMAN
33-89
57
2
A:33-89
B:33-89
57
57
1.5
ENST00000379923
5
ENSE00000832723
chr9:
32408512-32408649
138
ACOC_HUMAN
89-135
47
2
A:89-135
B:89-135
47
47
1.6
ENST00000379923
6
ENSE00000832724
chr9:
32418126-32418195
70
ACOC_HUMAN
135-158
24
2
A:135-158
B:135-158
24
24
1.7
ENST00000379923
7
ENSE00000832725
chr9:
32418326-32418509
184
ACOC_HUMAN
159-220
62
2
A:159-220
B:159-220
62
62
1.8
ENST00000379923
8
ENSE00001121894
chr9:
32419036-32419175
140
ACOC_HUMAN
220-266
47
2
A:220-266
B:220-266
47
47
1.9
ENST00000379923
9
ENSE00000832727
chr9:
32420854-32421025
172
ACOC_HUMAN
267-324
58
2
A:267-324
B:267-324
58
58
1.10
ENST00000379923
10
ENSE00000832728
chr9:
32423317-32423417
101
ACOC_HUMAN
324-357
34
2
A:324-357
B:324-357
34
34
1.11
ENST00000379923
11
ENSE00000832729
chr9:
32424547-32424663
117
ACOC_HUMAN
358-396
39
2
A:358-396
B:358-396
39
39
1.12b
ENST00000379923
12b
ENSE00000832730
chr9:
32425836-32425995
160
ACOC_HUMAN
397-450
54
2
A:397-450
B:397-450
54
54
1.13
ENST00000379923
13
ENSE00000832731
chr9:
32427299-32427434
136
ACOC_HUMAN
450-495
46
2
A:450-495
B:450-495
46
46
1.14
ENST00000379923
14
ENSE00000832732
chr9:
32429417-32429501
85
ACOC_HUMAN
495-523
29
2
A:495-523
B:495-523
29
29
1.15
ENST00000379923
15
ENSE00000832733
chr9:
32430416-32430572
157
ACOC_HUMAN
524-576
53
2
A:524-576
B:524-576
53
53
1.16
ENST00000379923
16
ENSE00000832734
chr9:
32431717-32431841
125
ACOC_HUMAN
576-617
42
2
A:576-617
B:576-617
42
42
1.17
ENST00000379923
17
ENSE00000832735
chr9:
32433726-32433830
105
ACOC_HUMAN
618-652
35
2
A:618-652
B:618-652
35
35
1.18
ENST00000379923
18
ENSE00000832736
chr9:
32434557-32434699
143
ACOC_HUMAN
653-700
48
2
A:653-700
B:653-700
48
48
1.20
ENST00000379923
20
ENSE00000832737
chr9:
32436248-32436395
148
ACOC_HUMAN
700-749
50
2
A:700-749
B:700-749
50
50
1.21
ENST00000379923
21
ENSE00000832738
chr9:
32440463-32440585
123
ACOC_HUMAN
750-790
41
2
A:750-790
B:750-790
41
41
1.22
ENST00000379923
22
ENSE00000832739
chr9:
32448894-32449079
186
ACOC_HUMAN
791-852
62
2
A:791-852
B:791-852
62
62
1.23a
ENST00000379923
23a
ENSE00001483092
chr9:
32449996-32450834
839
ACOC_HUMAN
853-889
37
2
A:853-889
B:853-889
37
37
[
close EXON info
]
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d2b3ya2 (A:2-630)
1b: SCOP_d2b3yb2 (B:2-630)
2a: SCOP_d2b3ya1 (A:631-889)
2b: SCOP_d2b3yb1 (B:631-889)
View:
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Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Aconitase iron-sulfur domain
(20)
Superfamily
:
Aconitase iron-sulfur domain
(20)
Family
:
Aconitase iron-sulfur domain
(20)
Protein domain
:
Iron-responsive element binding protein 1, N-terminal domain
(2)
Human (Homo sapiens) [TaxId: 9606]
(2)
1a
d2b3ya2
A:2-630
1b
d2b3yb2
B:2-630
Fold
:
The swivelling beta/beta/alpha domain
(136)
Superfamily
:
LeuD/IlvD-like
(25)
Family
:
LeuD-like
(19)
Protein domain
:
ron-responsive element binding protein 1, C-terminal domain
(2)
Human (Homo sapiens) [TaxId: 9606]
(2)
2a
d2b3ya1
A:631-889
2b
d2b3yb1
B:631-889
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
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Asymmetric Unit 1
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Asym.Unit (310 KB)
Header - Asym.Unit
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Header - Biol.Unit 1
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