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1YTM
Biol. Unit 1
Info
Asym.Unit (177 KB)
Biol.Unit 1 (88 KB)
Biol.Unit 2 (88 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF PHOSPHOENOLPYRUVATE CARBOXYKINASE OF ANAEROBIOSPIRILLUM SUCCINICIPRODUCENS COMPLEXED WITH ATP, OXALATE, MAGNESIUM AND MANGANESE IONS
Authors
:
L. T. J. Delbaere, J. J. H. Cotelesage
Date
:
10 Feb 05 (Deposition) - 24 Jan 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Kinase; Domain Closure; Nucleotide Binding; Parallel Beta Sheet-Like Hydrogen Bond, Lyase
(Keyword Search:
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Reference
:
J. J. H. Cotelesage, L. Prasad, J. G. Zeikus, M. Laivenieks, L. T. J. Delbaere
Crystal Structure Of Anaerobiospirillum Succiniciproducens Pep Carboxykinase Reveals An Important Active Site Loop
Int. J. Biochem. Cell Biol. V. 37 1829 2005
(for further references see the
PDB file header
)
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Hetero Components
(2, 2)
Info
All Hetero Components
1a: ADENOSINE-5'-TRIPHOSPHATE (ATPa)
1b: ADENOSINE-5'-TRIPHOSPHATE (ATPb)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
3a: MANGANESE (II) ION (MNa)
3b: MANGANESE (II) ION (MNb)
4a: OXALIC ACID (OXDa)
4b: OXALIC ACID (OXDb)
View:
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Label:
No.
Name
Count
Type
Full Name
1
ATP
1
Ligand/Ion
ADENOSINE-5'-TRIPHOSPHATE
2
MG
-1
Ligand/Ion
MAGNESIUM ION
3
MN
-1
Ligand/Ion
MANGANESE (II) ION
4
OXD
1
Ligand/Ion
OXALIC ACID
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC5 (SOFTWARE)
4: AC7 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
THR A:249 , ATP A:541 , HOH A:1002 , HOH A:1003 , HOH A:1222
BINDING SITE FOR RESIDUE MG A 998
2
AC2
SOFTWARE
LYS A:206 , HIS A:225 , ASP A:263 , ATP A:541 , OXD A:543
BINDING SITE FOR RESIDUE MN A 999
3
AC5
SOFTWARE
HIS A:225 , LEU A:243 , SER A:244 , GLY A:245 , THR A:246 , GLY A:247 , LYS A:248 , THR A:249 , THR A:250 , ASP A:263 , LYS A:282 , ARG A:327 , THR A:435 , ARG A:443 , ILE A:444 , ILE A:446 , THR A:449 , OXD A:543 , MG A:998 , MN A:999 , HOH A:1002 , HOH A:1003 , HOH A:1018 , HOH A:1033 , HOH A:1089
BINDING SITE FOR RESIDUE ATP A 541
4
AC7
SOFTWARE
ARG A:60 , TYR A:200 , LYS A:206 , HIS A:225 , SER A:244 , ASP A:263 , ARG A:327 , PHE A:407 , ATP A:541 , MN A:999 , HOH A:1041 , HOH A:1060 , HOH A:1224
BINDING SITE FOR RESIDUE OXD A 543
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: PEPCK_ATP (A:259-274)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PEPCK_ATP
PS00532
Phosphoenolpyruvate carboxykinase (ATP) signature.
PCKA_ANASU
259-274
1
A:259-274
-
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Exons
(0, 0)
Info
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1ytma1 (A:2-220)
1b: SCOP_d1ytmb1 (B:1002-1220)
2a: SCOP_d1ytma2 (A:221-518)
2b: SCOP_d1ytmb2 (B:1221-1518)
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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
:
automated matches
(6)
Protein domain
:
automated matches
(6)
Anaerobiospirillum succiniciproducens [TaxId: 13335]
(2)
1a
d1ytma1
A:2-220
1b
d1ytmb1
B:1002-1220
Fold
:
PEP carboxykinase-like
(61)
Superfamily
:
PEP carboxykinase-like
(61)
Family
:
automated matches
(7)
Protein domain
:
automated matches
(7)
Anaerobiospirillum succiniciproducens [TaxId: 13335]
(2)
2a
d1ytma2
A:221-518
2b
d1ytmb2
B:1221-1518
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CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_1ytmA01 (A:2-36,A:54-220)
1b: CATH_1ytmB01 (B:1002-1036,B:1054-1220)
2a: CATH_1ytmA03 (A:221-277,A:337-518)
2b: CATH_1ytmB03 (B:1221-1277,B:1337-1518)
3a: CATH_1ytmA02 (A:37-53,A:278-336)
3b: CATH_1ytmB02 (B:1037-1053,B:1278-1336)
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Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Phosphoenolpyruvate Carboxykinase; domain 1
(42)
Homologous Superfamily
:
Phosphoenolpyruvate Carboxykinase, domain 1
(42)
Anaerobiospirillum succiniciproducens. Organism_taxid: 13335.
(1)
1a
1ytmA01
A:2-36,A:54-220
1b
1ytmB01
B:1002-1036,B:1054-1220
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Phosphoenolpyruvate Carboxykinase; domain 3
(62)
Homologous Superfamily
:
[code=3.90.228.20, no name defined]
(42)
Anaerobiospirillum succiniciproducens. Organism_taxid: 13335.
(1)
2a
1ytmA03
A:221-277,A:337-518
2b
1ytmB03
B:1221-1277,B:1337-1518
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Complex
(381)
Topology
:
Phosphoenolpyruvate Carboxykinase; domain 2
(42)
Homologous Superfamily
:
Phosphoenolpyruvate Carboxykinase, domain 2
(42)
Anaerobiospirillum succiniciproducens. Organism_taxid: 13335.
(1)
3a
1ytmA02
A:37-53,A:278-336
3b
1ytmB02
B:1037-1053,B:1278-1336
[
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Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_PEPCK_ATP_1ytmB01 (B:1014-1487)
1b: PFAM_PEPCK_ATP_1ytmB02 (B:1014-1487)
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Clan
:
PEP-carboxyk
(36)
Family
:
PEPCK_ATP
(11)
Anaerobiospirillum succiniciproducens
(1)
1a
PEPCK_ATP-1ytmB01
B:1014-1487
1b
PEPCK_ATP-1ytmB02
B:1014-1487
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Chain A
Asymmetric Unit 1
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Asym.Unit (177 KB)
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