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1WOI
Asym. Unit
Info
Asym.Unit (292 KB)
Biol.Unit 1 (286 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF AGMATINASE REVEALS STRUCTURAL CONSERVATION AND INHIBITION MECHANISM OF THE UREOHYDROLASE SUPERFAMILY
Authors
:
H. J. Ahn, K. H. Kim, J. Lee, J. -Y. Ha, H. H. Lee, D. Kim, H. -J. Yoon, A. - R. Kwon, S. W. Suh
Date
:
18 Aug 04 (Deposition) - 07 Sep 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.85
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Alpha/Beta Fold, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. J. Ahn, K. H. Kim, J. Lee, J. -Y. Ha, H. H. Lee, D. Kim, H. -J. Yoon, A. -R. Kwon, S. W. Suh
Crystal Structure Of Agmatinase Reveals Structural Conservation And Inhibition Mechanism Of The Ureohydrolase Superfamily
J. Biol. Chem. V. 279 50505 2004
(for further references see the
PDB file header
)
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Hetero Components
(1, 12)
Info
All Hetero Components
1a: MANGANESE (II) ION (MNa)
1b: MANGANESE (II) ION (MNb)
1c: MANGANESE (II) ION (MNc)
1d: MANGANESE (II) ION (MNd)
1e: MANGANESE (II) ION (MNe)
1f: MANGANESE (II) ION (MNf)
1g: MANGANESE (II) ION (MNg)
1h: MANGANESE (II) ION (MNh)
1i: MANGANESE (II) ION (MNi)
1j: MANGANESE (II) ION (MNj)
1k: MANGANESE (II) ION (MNk)
1l: MANGANESE (II) ION (MNl)
View:
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Label:
No.
Name
Count
Type
Full Name
1
MN
12
Ligand/Ion
MANGANESE (II) ION
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Sites
(12, 12)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:121 , ASP A:143 , ASP A:147 , ASP A:229 , MN A:1502 , HOH A:1636
BINDING SITE FOR RESIDUE MN A 1501
02
AC2
SOFTWARE
ASP A:143 , HIS A:145 , ASP A:229 , ASP A:231 , MN A:1501 , HOH A:1636
BINDING SITE FOR RESIDUE MN A 1502
03
AC3
SOFTWARE
HIS B:121 , ASP B:143 , ASP B:147 , ASP B:229 , MN B:1504 , HOH B:1601
BINDING SITE FOR RESIDUE MN B 1503
04
AC4
SOFTWARE
ASP B:143 , HIS B:145 , ASP B:229 , ASP B:231 , MN B:1503 , HOH B:1601
BINDING SITE FOR RESIDUE MN B 1504
05
AC5
SOFTWARE
HIS C:121 , ASP C:143 , ASP C:147 , ASP C:229 , MN C:1506 , HOH C:1630
BINDING SITE FOR RESIDUE MN C 1505
06
AC6
SOFTWARE
ASP C:143 , HIS C:145 , ASP C:229 , ASP C:231 , MN C:1505 , HOH C:1630
BINDING SITE FOR RESIDUE MN C 1506
07
AC7
SOFTWARE
HIS D:121 , ASP D:143 , ASP D:147 , ASP D:229 , MN D:1508 , HOH D:1600
BINDING SITE FOR RESIDUE MN D 1507
08
AC8
SOFTWARE
ASP D:143 , HIS D:145 , ASP D:229 , ASP D:231 , MN D:1507 , HOH D:1600
BINDING SITE FOR RESIDUE MN D 1508
09
AC9
SOFTWARE
HIS E:121 , ASP E:143 , ASP E:147 , ASP E:229 , MN E:1510 , HOH E:1616
BINDING SITE FOR RESIDUE MN E 1509
10
BC1
SOFTWARE
ASP E:143 , HIS E:145 , ASP E:229 , ASP E:231 , MN E:1509 , HOH E:1616
BINDING SITE FOR RESIDUE MN E 1510
11
BC2
SOFTWARE
HIS F:121 , ASP F:143 , ASP F:147 , ASP F:229 , MN F:1512 , HOH F:1627
BINDING SITE FOR RESIDUE MN F 1511
12
BC3
SOFTWARE
ASP F:143 , HIS F:145 , ASP F:229 , ASP F:231 , MN F:1511 , HOH F:1627
BINDING SITE FOR RESIDUE MN F 1512
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
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End label:
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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
(1, 6)
Info
All SCOP Domains
1a: SCOP_d1woia_ (A:)
1b: SCOP_d1woib_ (B:)
1c: SCOP_d1woic_ (C:)
1d: SCOP_d1woid_ (D:)
1e: SCOP_d1woie_ (E:)
1f: SCOP_d1woif_ (F:)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Arginase/deacetylase
(138)
Superfamily
:
Arginase/deacetylase
(138)
Family
:
Arginase-like amidino hydrolases
(97)
Protein domain
:
Agmatinase
(3)
Deinococcus radiodurans [TaxId: 1299]
(3)
1a
d1woia_
A:
1b
d1woib_
B:
1c
d1woic_
C:
1d
d1woid_
D:
1e
d1woie_
E:
1f
d1woif_
F:
[
close SCOP info
]
CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_1woiA00 (A:3-305)
1b: CATH_1woiB00 (B:3-305)
1c: CATH_1woiC00 (C:3-305)
1d: CATH_1woiD00 (D:3-305)
1e: CATH_1woiE00 (E:3-305)
1f: CATH_1woiF00 (F:3-305)
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Homologous Superfamilies
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Arginase; Chain A
(84)
Homologous Superfamily
:
[code=3.40.800.10, no name defined]
(63)
Deinococcus radiodurans. Organism_taxid: 1299.
(3)
1a
1woiA00
A:3-305
1b
1woiB00
B:3-305
1c
1woiC00
C:3-305
1d
1woiD00
D:3-305
1e
1woiE00
E:3-305
1f
1woiF00
F:3-305
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Pfam Domains
(1, 6)
Info
all PFAM domains
1a: PFAM_Arginase_1woiF01 (F:29-298)
1b: PFAM_Arginase_1woiF02 (F:29-298)
1c: PFAM_Arginase_1woiF03 (F:29-298)
1d: PFAM_Arginase_1woiF04 (F:29-298)
1e: PFAM_Arginase_1woiF05 (F:29-298)
1f: PFAM_Arginase_1woiF06 (F:29-298)
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Clans
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Organisms
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)
(
)
Clan
:
Arginase
(56)
Family
:
Arginase
(37)
Deinococcus radiodurans
(3)
1a
Arginase-1woiF01
F:29-298
1b
Arginase-1woiF02
F:29-298
1c
Arginase-1woiF03
F:29-298
1d
Arginase-1woiF04
F:29-298
1e
Arginase-1woiF05
F:29-298
1f
Arginase-1woiF06
F:29-298
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Asymmetric Unit 1
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select residue range 5 to 10 in all chains
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Asym.Unit (292 KB)
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