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1YP3
Asym. Unit
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Asym.Unit (288 KB)
Biol.Unit 1 (280 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF POTATO TUBER ADP-GLUCOSE PYROPHOSPHORYLASE IN COMPLEX WITH ATP
Authors
:
X. Jin, M. A. Ballicora, J. Preiss, J. H. Geiger
Date
:
29 Jan 05 (Deposition) - 15 Mar 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Adp-Glucose Pyrophosphorylase, Adp-Glucose Synthase, Agpase B, Alpha-D-Glucose-1-Phosphate Adenyl Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
X. Jin, M. A. Ballicora, J. Preiss, J. H. Geiger
Crystal Structure Of Potato Tuber Adp-Glucose Pyrophosphorylase.
Embo J. V. 24 694 2005
(for further references see the
PDB file header
)
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Hetero Components
(2, 15)
Info
All Hetero Components
1a: ADENOSINE-5'-TRIPHOSPHATE (ATPa)
1b: ADENOSINE-5'-TRIPHOSPHATE (ATPb)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
2d: SULFATE ION (SO4d)
2e: SULFATE ION (SO4e)
2f: SULFATE ION (SO4f)
2g: SULFATE ION (SO4g)
2h: SULFATE ION (SO4h)
2i: SULFATE ION (SO4i)
2j: SULFATE ION (SO4j)
2k: SULFATE ION (SO4k)
2l: SULFATE ION (SO4l)
2m: SULFATE ION (SO4m)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ATP
2
Ligand/Ion
ADENOSINE-5'-TRIPHOSPHATE
2
SO4
13
Ligand/Ion
SULFATE ION
[
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Sites
(15, 15)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:41 , PRO A:47 , ARG A:53 , SER A:80 , ASP A:370 , LYS A:404 , LYS A:441
BINDING SITE FOR RESIDUE SO4 A 1000
02
AC2
SOFTWARE
ARG B:41 , ARG B:53 , SER B:80 , ASP B:370 , LYS B:404 , LYS B:441 , HOH B:1054
BINDING SITE FOR RESIDUE SO4 B 1001
03
AC3
SOFTWARE
ARG C:41 , ARG C:53 , SER C:80 , ASP C:370 , LYS C:404 , LYS C:441
BINDING SITE FOR RESIDUE SO4 C 1002
04
AC4
SOFTWARE
ARG D:41 , ARG D:53 , ASP D:370 , LYS D:404 , LYS D:441
BINDING SITE FOR RESIDUE SO4 D 1003
05
AC5
SOFTWARE
ARG B:83 , LYS C:69 , HIS C:134 , THR C:135 , HOH C:1023
BINDING SITE FOR RESIDUE SO4 C 1005
06
AC6
SOFTWARE
LYS B:69 , HIS B:134 , THR B:135 , HOH B:1021
BINDING SITE FOR RESIDUE SO4 B 1006
07
AC7
SOFTWARE
LYS A:69 , GLU A:133 , HIS A:134 , THR A:135
BINDING SITE FOR RESIDUE SO4 A 1007
08
AC8
SOFTWARE
ARG A:53 , HIS A:84 , GLN A:314 , ARG A:316 , HOH A:1068
BINDING SITE FOR RESIDUE SO4 A 1008
09
AC9
SOFTWARE
ARG B:53 , HIS B:84 , GLN B:314 , ARG B:316
BINDING SITE FOR RESIDUE SO4 B 1009
10
BC1
SOFTWARE
ARG C:53 , HIS C:84 , GLN C:314 , ARG C:316 , HOH C:1074
BINDING SITE FOR RESIDUE SO4 C 1010
11
BC2
SOFTWARE
ARG D:53 , HIS D:84 , GLN D:314 , ARG D:316 , LYS D:404 , HOH D:1034 , HOH D:1038
BINDING SITE FOR RESIDUE SO4 D 1011
12
BC3
SOFTWARE
GLY A:29 , GLY A:31 , THR A:32 , ARG A:33 , LYS A:43 , ATP A:757
BINDING SITE FOR RESIDUE SO4 A 1020
13
BC4
SOFTWARE
GLY C:28 , GLY C:29 , ALA C:30 , GLY C:31 , THR C:32 , ARG C:33 , LYS C:43
BINDING SITE FOR RESIDUE SO4 C 1022
14
BC5
SOFTWARE
LEU A:26 , GLY A:28 , LYS A:43 , LEU A:73 , GLN A:118 , GLY A:119 , THR A:120 , ALA A:123 , ALA A:143 , GLY A:144 , ASP A:145 , ASP A:253 , PHE A:254 , GLY A:255 , SER A:256 , SO4 A:1020 , HOH A:1023 , HOH A:1085
BINDING SITE FOR RESIDUE ATP A 757
15
BC6
SOFTWARE
LEU C:26 , GLY C:27 , GLY C:28 , GLY C:29 , LYS C:43 , LEU C:73 , GLN C:118 , GLY C:119 , THR C:120 , ALA C:143 , GLY C:144 , ASP C:145 , HIS C:146 , GLY C:231 , ASP C:253 , PHE C:254 , GLY C:255 , SER C:256 , HOH C:1034 , HOH C:1110
BINDING SITE FOR RESIDUE ATP C 758
[
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]
SAPs(SNPs)/Variants
(1, 4)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_GLGS_SOLTU_001 (I450V, chain A/B/C/D, )
View:
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Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_GLGS_SOLTU_001
*
I
520
V
GLGS_SOLTU
---
---
A/B/C/D
I
450
V
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 12)
Info
All PROSITE Patterns/Profiles
1: ADP_GLC_PYROPHOSPH_1 (A:27-46,B:27-46,C:27-46,D:27-46)
2: ADP_GLC_PYROPHOSPH_2 (A:116-124,B:118-124,C:116-124,D:11...)
3: ADP_GLC_PYROPHOSPH_3 (A:228-238,B:228-238,C:228-238,D:22...)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ADP_GLC_PYROPHOSPH_1
PS00808
ADP-glucose pyrophosphorylase signature 1.
GLGS_SOLTU
97-116
4
A:27-46
B:27-46
C:27-46
D:27-46
2
ADP_GLC_PYROPHOSPH_2
PS00809
ADP-glucose pyrophosphorylase signature 2.
GLGS_SOLTU
186-194
4
A:116-124
B:118-124
C:116-124
D:119-124
3
ADP_GLC_PYROPHOSPH_3
PS00810
ADP-glucose pyrophosphorylase signature 3.
GLGS_SOLTU
298-308
4
A:228-238
B:228-238
C:228-238
D:228-238
[
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]
Exons
(0, 0)
Info
All Exons
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1yp3a1 (A:317-451)
1b: SCOP_d1yp3c1 (C:317-451)
1c: SCOP_d1yp3d1 (D:317-451)
1d: SCOP_d1yp3b1 (B:317-451)
2a: SCOP_d1yp3a2 (A:10-316)
2b: SCOP_d1yp3c2 (C:10-316)
2c: SCOP_d1yp3d2 (D:13-316)
2d: SCOP_d1yp3b2 (B:11-316)
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Class
:
All beta proteins
(24004)
Fold
:
Single-stranded left-handed beta-helix
(154)
Superfamily
:
Trimeric LpxA-like enzymes
(147)
Family
:
GlmU C-terminal domain-like
(22)
Protein domain
:
Glucose-1-phosphate adenylyltransferase small subunit, C-terminal domain
(3)
Potato (Solanum tuberosum) [TaxId: 4113]
(3)
1a
d1yp3a1
A:317-451
1b
d1yp3c1
C:317-451
1c
d1yp3d1
D:317-451
1d
d1yp3b1
B:317-451
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Nucleotide-diphospho-sugar transferases
(408)
Superfamily
:
Nucleotide-diphospho-sugar transferases
(408)
Family
:
glucose-1-phosphate thymidylyltransferase
(43)
Protein domain
:
Glucose-1-phosphate adenylyltransferase small subunit, catalytic domain
(3)
Potato (Solanum tuberosum) [TaxId: 4113]
(3)
2a
d1yp3a2
A:10-316
2b
d1yp3c2
C:10-316
2c
d1yp3d2
D:13-316
2d
d1yp3b2
B:11-316
[
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CATH Domains
(0, 0)
Info
all CATH domains
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_NTP_transferase_1yp3D01 (D:22-297)
1b: PFAM_NTP_transferase_1yp3D02 (D:22-297)
1c: PFAM_NTP_transferase_1yp3D03 (D:22-297)
1d: PFAM_NTP_transferase_1yp3D04 (D:22-297)
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Clan
:
GT-A
(172)
Family
:
NTP_transferase
(15)
Solanum tuberosum (Potato)
(3)
1a
NTP_transferase-1yp3D01
D:22-297
1b
NTP_transferase-1yp3D02
D:22-297
1c
NTP_transferase-1yp3D03
D:22-297
1d
NTP_transferase-1yp3D04
D:22-297
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