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1J3B
Asym. Unit
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Asym.Unit (187 KB)
Biol.Unit 1 (182 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF ATP-DEPENDENT PHOSPHOENOLPYRUVATE CARBOXYKINASE FROM THERMUS THERMOPHILUS HB8
Authors
:
M. Sugahara, M. Miyano, N. Kunishima, Riken Structural Genomics/Pr Initiative (Rsgi)
Date
:
21 Jan 03 (Deposition) - 11 Feb 03 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Phosphoenolpyruvate Carboxykinase, Adenosine Triphosphate, Thermus Thermophilus, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Sugahara, N. Ohshima, Y. Ukita, M. Sugahara, N. Kunishima
Structure Of Atp-Dependent Phosphoenolpyruvate Carboxykinas From Thermus Thermophilus Hb8 Showing The Structural Basis Of Induced Fit And Thermostability.
Acta Crystallogr. , Sect. D V. 61 1500 2005
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Hetero Components
(3, 13)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
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)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
2
Ligand/Ion
CALCIUM ION
2
GOL
2
Ligand/Ion
GLYCEROL
3
PO4
9
Ligand/Ion
PHOSPHATE ION
[
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Sites
(13, 13)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:130 , ASN A:131 , PHE A:133 , GLY A:267 , HOH A:3030
BINDING SITE FOR RESIDUE CA A 1001
02
AC2
SOFTWARE
ARG B:130 , ASN B:131 , PHE B:133 , GLY B:267 , HOH B:3104
BINDING SITE FOR RESIDUE CA B 1002
03
AC3
SOFTWARE
VAL A:20 , SER A:21 , ARG A:130 , ARG A:137 , HOH A:3016 , HOH A:3020 , HOH A:3028 , HIS B:38
BINDING SITE FOR RESIDUE PO4 A 2001
04
AC4
SOFTWARE
LYS A:413 , LYS A:416 , HIS A:417 , HOH A:3145
BINDING SITE FOR RESIDUE PO4 A 2002
05
AC5
SOFTWARE
LEU A:233 , SER A:234 , GLY A:235 , THR A:236 , GLY A:237 , LYS A:238 , THR A:239 , LYS A:272 , HOH A:3176 , HOH A:3286
BINDING SITE FOR RESIDUE PO4 A 2003
06
AC6
SOFTWARE
ARG A:340 , HOH A:3045 , HOH A:3190
BINDING SITE FOR RESIDUE PO4 A 2004
07
AC7
SOFTWARE
HIS A:38 , HOH A:3040 , HOH A:3052 , HOH A:3127 , SER B:21 , PRO B:22 , ARG B:130 , ARG B:137 , HOH B:3261
BINDING SITE FOR RESIDUE PO4 B 2005
08
AC8
SOFTWARE
GLU B:259 , LYS B:413 , LYS B:416 , HIS B:417 , HOH B:3310
BINDING SITE FOR RESIDUE PO4 B 2006
09
AC9
SOFTWARE
LEU B:233 , SER B:234 , GLY B:235 , THR B:236 , GLY B:237 , LYS B:238 , THR B:239 , HOH B:3178 , HOH B:3184 , HOH B:3246 , HOH B:3248
BINDING SITE FOR RESIDUE PO4 B 2007
10
BC1
SOFTWARE
GLU B:5 , HIS B:10 , LYS B:12 , HOH B:3314
BINDING SITE FOR RESIDUE PO4 B 2008
11
BC2
SOFTWARE
ARG B:111 , ARG B:210
BINDING SITE FOR RESIDUE PO4 B 2009
12
BC3
SOFTWARE
TYR A:93 , GLN A:161 , ARG A:166 , HOH A:3164
BINDING SITE FOR RESIDUE GOL A 3001
13
BC4
SOFTWARE
PHE B:160 , GLN B:161 , ARG B:166 , HOH B:3097 , HOH B:3243
BINDING SITE FOR RESIDUE GOL B 3002
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: PEPCK_ATP (A:249-264,B:249-264)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PEPCK_ATP
PS00532
Phosphoenolpyruvate carboxykinase (ATP) signature.
PCKA_THET8
249-264
2
A:249-264
B:249-264
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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, 4)
Info
All SCOP Domains
1a: SCOP_d1j3ba2 (A:2-211)
1b: SCOP_d1j3bb2 (B:2-211)
2a: SCOP_d1j3ba1 (A:212-529)
2b: SCOP_d1j3bb1 (B:212-528)
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Classes
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)
(
)
Folds
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)
(
)
Superfamilies
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)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
PEP carboxykinase N-terminal domain
(54)
Superfamily
:
PEP carboxykinase N-terminal domain
(54)
Family
:
PEP carboxykinase N-terminal domain
(48)
Protein domain
:
Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase)
(16)
Thermus thermophilus [TaxId: 274]
(3)
1a
d1j3ba2
A:2-211
1b
d1j3bb2
B:2-211
Fold
:
PEP carboxykinase-like
(61)
Superfamily
:
PEP carboxykinase-like
(61)
Family
:
PEP carboxykinase C-terminal domain
(48)
Protein domain
:
Phosphoenolpyruvate (PEP) carboxykinase (ATP-oxaloacetate carboxy-lyase)
(16)
Thermus thermophilus [TaxId: 274]
(3)
2a
d1j3ba1
A:212-529
2b
d1j3bb1
B:212-528
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CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_1j3bB01 (B:2-33,B:55-211)
1b: CATH_1j3bA01 (A:2-33,A:55-211)
2a: CATH_1j3bA03 (A:212-267,A:330-526)
2b: CATH_1j3bB03 (B:212-267,B:330-526)
3a: CATH_1j3bA02 (A:34-50,A:268-327)
3b: CATH_1j3bB02 (B:34-50,B:268-327)
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)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Phosphoenolpyruvate Carboxykinase; domain 1
(42)
Homologous Superfamily
:
Phosphoenolpyruvate Carboxykinase, domain 1
(42)
Thermus thermophilus hb8. Organism_taxid: 300852. Strain: hb8.
(3)
1a
1j3bB01
B:2-33,B:55-211
1b
1j3bA01
A:2-33,A:55-211
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Phosphoenolpyruvate Carboxykinase; domain 3
(62)
Homologous Superfamily
:
[code=3.90.228.20, no name defined]
(42)
Thermus thermophilus hb8. Organism_taxid: 300852. Strain: hb8.
(3)
2a
1j3bA03
A:212-267,A:330-526
2b
1j3bB03
B:212-267,B:330-526
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Complex
(381)
Topology
:
Phosphoenolpyruvate Carboxykinase; domain 2
(42)
Homologous Superfamily
:
Phosphoenolpyruvate Carboxykinase, domain 2
(42)
Thermus thermophilus hb8. Organism_taxid: 300852. Strain: hb8.
(3)
3a
1j3bA02
A:34-50,A:268-327
3b
1j3bB02
B:34-50,B:268-327
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Pfam Domains
(0, 0)
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Asymmetric Unit 1
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