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3WGD
Asym. Unit
Info
Asym.Unit (361 KB)
Biol.Unit 1 (43 KB)
Biol.Unit 2 (42 KB)
Biol.Unit 3 (43 KB)
Biol.Unit 4 (42 KB)
Biol.Unit 5 (42 KB)
Biol.Unit 6 (42 KB)
Biol.Unit 7 (42 KB)
Biol.Unit 8 (42 KB)
Biol.Unit 9 (43 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF ERP46 TRX1
Authors
:
K. Inaba, M. Suzuki, R. Kojima
Date
:
04 Aug 13 (Deposition) - 25 Jun 14 (Release) - 25 Jun 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Biol. Unit 5: E (1x)
Biol. Unit 6: F (1x)
Biol. Unit 7: G (1x)
Biol. Unit 8: H (1x)
Biol. Unit 9: I (1x)
Keywords
:
Pdi Family Member, Thioredoxin Domain, Protein Disulfide Isomerase, Isomerase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. Kojima, M. Okumura, S. Masui, S. Kanemura, M. Inoue, M. Saiki, H. Yamaguchi, T. Hikima, M. Suzuki, S. Akiyama, K. Inaba
Radically Different Thioredoxin Domain Arrangement Of Erp46 An Efficient Disulfide Bond Introducer Of The Mammalian Pdi Family
Structure V. 22 431 2014
[
close entry info
]
Hetero Components
(3, 31)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
1d: GLYCEROL (GOLd)
1e: GLYCEROL (GOLe)
1f: GLYCEROL (GOLf)
1g: GLYCEROL (GOLg)
1h: GLYCEROL (GOLh)
1i: GLYCEROL (GOLi)
1j: GLYCEROL (GOLj)
1k: GLYCEROL (GOLk)
2a: POTASSIUM ION (Ka)
2b: POTASSIUM ION (Kb)
2c: POTASSIUM ION (Kc)
2d: POTASSIUM ION (Kd)
2e: POTASSIUM ION (Ke)
3a: PHOSPHATE ION (PO4a)
3b: PHOSPHATE ION (PO4b)
3c: PHOSPHATE ION (PO4c)
3d: PHOSPHATE ION (PO4d)
3e: PHOSPHATE ION (PO4e)
3f: PHOSPHATE ION (PO4f)
3g: PHOSPHATE ION (PO4g)
3h: PHOSPHATE ION (PO4h)
3i: PHOSPHATE ION (PO4i)
3j: PHOSPHATE ION (PO4j)
3k: PHOSPHATE ION (PO4k)
3l: PHOSPHATE ION (PO4l)
3m: PHOSPHATE ION (PO4m)
3n: PHOSPHATE ION (PO4n)
3o: PHOSPHATE ION (PO4o)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
11
Ligand/Ion
GLYCEROL
2
K
5
Ligand/Ion
POTASSIUM ION
3
PO4
15
Ligand/Ion
PHOSPHATE ION
[
close Hetero Component info
]
Sites
(31, 31)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER A:129 , ARG A:134 , HOH A:331 , HOH A:337 , THR F:67 , ALA F:68 , ASP F:69 , HIS F:124
BINDING SITE FOR RESIDUE PO4 A 201
02
AC2
SOFTWARE
THR A:67 , ALA A:68 , ASP A:69 , HIS A:124 , HOH A:320 , HOH A:340
BINDING SITE FOR RESIDUE PO4 A 202
03
AC3
SOFTWARE
PRO A:154 , ARG A:155
BINDING SITE FOR RESIDUE PO4 A 203
04
AC4
SOFTWARE
GLN A:146 , GLU A:147
BINDING SITE FOR RESIDUE PO4 A 204
05
AC5
SOFTWARE
ALA A:123 , HIS A:124 , HOH A:318 , HOH A:336
BINDING SITE FOR RESIDUE GOL A 205
06
AC6
SOFTWARE
ARG A:134
BINDING SITE FOR RESIDUE GOL A 206
07
AC7
SOFTWARE
TYR A:151 , GLN A:152 , GLY A:153 , ARG A:155
BINDING SITE FOR RESIDUE GOL A 207
08
AC8
SOFTWARE
THR B:67 , ALA B:68 , ASP B:69 , HIS B:124 , HOH B:323
BINDING SITE FOR RESIDUE PO4 B 201
09
AC9
SOFTWARE
SER B:77 , HOH B:315 , LYS F:113
BINDING SITE FOR RESIDUE GOL B 202
10
BC1
SOFTWARE
LEU B:65 , THR B:67 , HIS B:124 , HOH B:312
BINDING SITE FOR RESIDUE GOL B 203
11
BC2
SOFTWARE
THR C:67 , ALA C:68 , ASP C:69 , HIS C:124 , HOH C:327
BINDING SITE FOR RESIDUE PO4 C 201
12
BC3
SOFTWARE
HIS C:60 , LYS C:63 , ASN C:100
BINDING SITE FOR RESIDUE PO4 C 202
13
BC4
SOFTWARE
LEU C:65 , THR C:67 , ALA C:123 , HIS C:124 , HOH C:331 , HOH C:334
BINDING SITE FOR RESIDUE GOL C 203
14
BC5
SOFTWARE
HIS C:64 , LEU C:65 , TYR C:66 , HOH C:320
BINDING SITE FOR RESIDUE K C 204
15
BC6
SOFTWARE
GLN C:146
BINDING SITE FOR RESIDUE K C 205
16
BC7
SOFTWARE
THR D:67 , ALA D:68 , ASP D:69 , HIS D:124
BINDING SITE FOR RESIDUE PO4 D 201
17
BC8
SOFTWARE
ARG D:134 , HOH D:318
BINDING SITE FOR RESIDUE PO4 D 202
18
BC9
SOFTWARE
SER B:129 , ARG B:134 , HOH B:311 , HOH B:317 , THR E:67 , ALA E:68 , ASP E:69 , HIS E:124
BINDING SITE FOR RESIDUE PO4 E 201
19
CC1
SOFTWARE
SER B:125 , ASP B:126 , SER B:129 , HOH B:311 , LEU E:65 , THR E:67 , HIS E:124 , HOH E:302
BINDING SITE FOR RESIDUE GOL E 202
20
CC2
SOFTWARE
CYS B:128 , TYR B:136 , THR E:67 , MET E:70
BINDING SITE FOR RESIDUE K E 203
21
CC3
SOFTWARE
SER A:125 , ASP A:126 , HOH A:350 , TYR F:66 , ALA F:123 , HIS F:124 , HOH F:304 , HOH F:331
BINDING SITE FOR RESIDUE GOL F 201
22
CC4
SOFTWARE
THR A:122 , HOH A:314 , TYR F:66 , ASN F:107 , TYR F:115 , HOH F:327
BINDING SITE FOR RESIDUE K F 202
23
CC5
SOFTWARE
PRO C:154 , ARG C:155 , GLY G:90 , GLN G:93 , ARG G:94
BINDING SITE FOR RESIDUE PO4 G 201
24
CC6
SOFTWARE
THR G:67 , ALA G:68 , ASP G:69 , HIS G:124 , HOH G:309 , HOH G:317 , SER H:129 , ARG H:134
BINDING SITE FOR RESIDUE PO4 G 202
25
CC7
SOFTWARE
LEU G:65 , THR G:67 , ASP G:120 , ALA G:123 , HIS G:124 , SER H:125 , ASP H:126
BINDING SITE FOR RESIDUE GOL G 203
26
CC8
SOFTWARE
THR H:67 , ALA H:68 , ASP H:69 , HIS H:124 , GOL H:202
BINDING SITE FOR RESIDUE PO4 H 201
27
CC9
SOFTWARE
TYR H:66 , THR H:67 , HIS H:124 , PO4 H:201 , HOH H:301 , HOH H:309 , HOH H:314
BINDING SITE FOR RESIDUE GOL H 202
28
DC1
SOFTWARE
GLN I:146 , GLU I:147
BINDING SITE FOR RESIDUE PO4 I 201
29
DC2
SOFTWARE
THR I:67 , ALA I:68 , ASP I:69 , HIS I:124 , HOH I:316
BINDING SITE FOR RESIDUE PO4 I 202
30
DC3
SOFTWARE
THR I:67 , HIS I:124 , HOH I:304
BINDING SITE FOR RESIDUE GOL I 203
31
DC4
SOFTWARE
ASP I:69 , HIS I:73
BINDING SITE FOR RESIDUE K I 204
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 18)
Info
All PROSITE Patterns/Profiles
1: THIOREDOXIN_2 (-|A:170-170,B:170-170,C:170-170,D:...)
2: THIOREDOXIN_1 (A:81-99,B:81-99,C:81-99,D:81-99,E:...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
THIOREDOXIN_2
PS51352
Thioredoxin domain profile.
TXND5_HUMAN
36-169
170-295
304-429
9
-
A:170-170
B:170-170
C:170-170
D:170-170
E:170-170
F:170-170
G:170-170
H:170-170
I:170-170
-
2
THIOREDOXIN_1
PS00194
Thioredoxin family active site.
TXND5_HUMAN
81-99
209-227
342-360
9
A:81-99
B:81-99
C:81-99
D:81-99
E:81-99
F:81-99
G:81-99
H:81-99
I:81-99
-
-
[
close PROSITE info
]
Exons
(3, 27)
Info
All Exons
Exon 1.1 (A:60-88 | B:60-88 | C:59-88 | D:60...)
Exon 1.3 (A:88-138 | B:88-138 | C:88-138 | D...)
Exon 1.4b (A:138-170 | B:138-170 | C:138-170 ...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/1.3
3: Boundary 1.3/1.4b
4: Boundary 1.4b/1.5b
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
ENST00000379757
1
ENSE00001482400
chr6:
7911047-7910747
301
TXND5_HUMAN
1-88
88
9
A:60-88
B:60-88
C:59-88
D:60-88
E:60-88
F:60-88
G:60-88
H:61-88
I:60-88
29
29
30
29
29
29
29
28
29
1.3
ENST00000379757
3
ENSE00002035816
chr6:
7904956-7904807
150
TXND5_HUMAN
88-138
51
9
A:88-138
B:88-138
C:88-138
D:88-138
E:88-138
F:88-138 (gaps)
G:88-138 (gaps)
H:88-138
I:88-138
51
51
51
51
51
51
51
51
51
1.4b
ENST00000379757
4b
ENSE00002030712
chr6:
7899914-7899809
106
TXND5_HUMAN
138-173
36
9
A:138-170
B:138-170
C:138-170
D:138-170
E:138-170
F:138-170
G:138-170
H:138-170
I:138-170
33
33
33
33
33
33
33
33
33
1.5b
ENST00000379757
5b
ENSE00002020031
chr6:
7895435-7895339
97
TXND5_HUMAN
174-206
33
0
-
-
1.6
ENST00000379757
6
ENSE00002062288
chr6:
7891969-7891854
116
TXND5_HUMAN
206-244
39
0
-
-
1.7
ENST00000379757
7
ENSE00002051337
chr6:
7889814-7889728
87
TXND5_HUMAN
245-273
29
0
-
-
1.8c
ENST00000379757
8c
ENSE00002072823
chr6:
7889081-7888938
144
TXND5_HUMAN
274-321
48
0
-
-
1.9
ENST00000379757
9
ENSE00002061487
chr6:
7886276-7886194
83
TXND5_HUMAN
322-349
28
0
-
-
1.10
ENST00000379757
10
ENSE00002026226
chr6:
7884721-7884592
130
TXND5_HUMAN
349-392
44
0
-
-
1.11c
ENST00000379757
11c
ENSE00001964269
chr6:
7883499-7881750
1750
TXND5_HUMAN
393-432
40
0
-
-
[
close EXON info
]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
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Sorry, no Info available
[
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
[
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Atom Selection
(currently selected atoms:
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)
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Nucleic
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All Atoms
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Protein & NOT PROSITE
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Chain C
Chain D
Chain E
Chain F
Chain G
Chain H
Chain I
Asymmetric Unit 1
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