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1WOG
Asym. Unit
Info
Asym.Unit (297 KB)
Biol.Unit 1 (292 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
:
1.80
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
(2, 18)
Info
All Hetero Components
1a: HEXANE-1,6-DIAMINE (16Da)
1b: HEXANE-1,6-DIAMINE (16Db)
1c: HEXANE-1,6-DIAMINE (16Dc)
1d: HEXANE-1,6-DIAMINE (16Dd)
1e: HEXANE-1,6-DIAMINE (16De)
1f: HEXANE-1,6-DIAMINE (16Df)
2a: MANGANESE (II) ION (MNa)
2b: MANGANESE (II) ION (MNb)
2c: MANGANESE (II) ION (MNc)
2d: MANGANESE (II) ION (MNd)
2e: MANGANESE (II) ION (MNe)
2f: MANGANESE (II) ION (MNf)
2g: MANGANESE (II) ION (MNg)
2h: MANGANESE (II) ION (MNh)
2i: MANGANESE (II) ION (MNi)
2j: MANGANESE (II) ION (MNj)
2k: MANGANESE (II) ION (MNk)
2l: MANGANESE (II) ION (MNl)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
16D
6
Ligand/Ion
HEXANE-1,6-DIAMINE
2
MN
12
Ligand/Ion
MANGANESE (II) ION
[
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Sites
(18, 18)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:121 , ASP A:143 , ASP A:147 , ASP A:229 , 16D A:1401 , MN A:1602
BINDING SITE FOR RESIDUE MN A 1601
02
AC2
SOFTWARE
ASP A:143 , HIS A:145 , ASP A:229 , ASP A:231 , 16D A:1401 , MN A:1601
BINDING SITE FOR RESIDUE MN A 1602
03
AC3
SOFTWARE
HIS B:121 , ASP B:143 , ASP B:147 , ASP B:229 , 16D B:1402 , MN B:1604
BINDING SITE FOR RESIDUE MN B 1603
04
AC4
SOFTWARE
ASP B:143 , HIS B:145 , ASP B:229 , ASP B:231 , 16D B:1402 , MN B:1603
BINDING SITE FOR RESIDUE MN B 1604
05
AC5
SOFTWARE
HIS C:121 , ASP C:143 , ASP C:147 , ASP C:229 , 16D C:1403 , MN C:1606
BINDING SITE FOR RESIDUE MN C 1605
06
AC6
SOFTWARE
ASP C:143 , HIS C:145 , ASP C:229 , ASP C:231 , 16D C:1403 , MN C:1605
BINDING SITE FOR RESIDUE MN C 1606
07
AC7
SOFTWARE
HIS D:121 , ASP D:143 , ASP D:147 , ASP D:229 , 16D D:1404 , MN D:1608
BINDING SITE FOR RESIDUE MN D 1607
08
AC8
SOFTWARE
ASP D:143 , HIS D:145 , ASP D:229 , ASP D:231 , 16D D:1404 , MN D:1607
BINDING SITE FOR RESIDUE MN D 1608
09
AC9
SOFTWARE
HIS E:121 , ASP E:143 , ASP E:147 , ASP E:229 , 16D E:1405 , MN E:1610
BINDING SITE FOR RESIDUE MN E 1609
10
BC1
SOFTWARE
ASP E:143 , HIS E:145 , ASP E:229 , ASP E:231 , 16D E:1405 , MN E:1609
BINDING SITE FOR RESIDUE MN E 1610
11
BC2
SOFTWARE
HIS F:121 , ASP F:143 , ASP F:147 , ASP F:229 , 16D F:1406 , MN F:1612
BINDING SITE FOR RESIDUE MN F 1611
12
BC3
SOFTWARE
ASP F:143 , HIS F:145 , ASP F:229 , ASP F:231 , 16D F:1406 , MN F:1611
BINDING SITE FOR RESIDUE MN F 1612
13
BC4
SOFTWARE
HIS A:145 , ASP A:147 , ASN A:159 , SER A:160 , ASP A:229 , ASP A:231 , MN A:1601 , MN A:1602 , HOH A:1620 , HOH A:1672 , HOH A:1680
BINDING SITE FOR RESIDUE 16D A 1401
14
BC5
SOFTWARE
HIS B:145 , ASP B:147 , ASN B:159 , SER B:160 , ASP B:229 , ASP B:231 , MN B:1603 , MN B:1604 , HOH B:1605 , HOH B:1636 , HOH B:1723
BINDING SITE FOR RESIDUE 16D B 1402
15
BC6
SOFTWARE
HIS C:145 , ASP C:147 , ASN C:159 , SER C:160 , ASP C:229 , ASP C:231 , MN C:1605 , MN C:1606 , HOH C:1629 , HOH C:1686 , HOH C:1712
BINDING SITE FOR RESIDUE 16D C 1403
16
BC7
SOFTWARE
HIS D:145 , ASP D:147 , ASN D:159 , SER D:160 , ASP D:229 , ASP D:231 , MN D:1607 , MN D:1608 , HOH D:1611 , HOH D:1654 , HOH D:1675
BINDING SITE FOR RESIDUE 16D D 1404
17
BC8
SOFTWARE
HIS E:145 , ASP E:147 , ASN E:159 , SER E:160 , ASP E:229 , ASP E:231 , MN E:1609 , MN E:1610 , HOH E:1679 , HOH E:1689
BINDING SITE FOR RESIDUE 16D E 1405
18
BC9
SOFTWARE
HIS F:145 , ASP F:147 , ASN F:159 , SER F:160 , ASP F:229 , ASP F:231 , MN F:1611 , MN F:1612 , HOH F:1654 , HOH F:1670
BINDING SITE FOR RESIDUE 16D F 1406
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
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Exons
(0, 0)
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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_d1woga_ (A:)
1b: SCOP_d1woge_ (E:)
1c: SCOP_d1wogf_ (F:)
1d: SCOP_d1wogb_ (B:)
1e: SCOP_d1wogc_ (C:)
1f: SCOP_d1wogd_ (D:)
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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
d1woga_
A:
1b
d1woge_
E:
1c
d1wogf_
F:
1d
d1wogb_
B:
1e
d1wogc_
C:
1f
d1wogd_
D:
[
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CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_1wogA00 (A:3-305)
1b: CATH_1wogE00 (E:3-305)
1c: CATH_1wogF00 (F:3-305)
1d: CATH_1wogB00 (B:3-305)
1e: CATH_1wogC00 (C:3-305)
1f: CATH_1wogD00 (D: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
1wogA00
A:3-305
1b
1wogE00
E:3-305
1c
1wogF00
F:3-305
1d
1wogB00
B:3-305
1e
1wogC00
C:3-305
1f
1wogD00
D:3-305
[
close CATH info
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Pfam Domains
(1, 6)
Info
all PFAM domains
1a: PFAM_Arginase_1wogF01 (F:29-298)
1b: PFAM_Arginase_1wogF02 (F:29-298)
1c: PFAM_Arginase_1wogF03 (F:29-298)
1d: PFAM_Arginase_1wogF04 (F:29-298)
1e: PFAM_Arginase_1wogF05 (F:29-298)
1f: PFAM_Arginase_1wogF06 (F:29-298)
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Clan
:
Arginase
(56)
Family
:
Arginase
(37)
Deinococcus radiodurans
(3)
1a
Arginase-1wogF01
F:29-298
1b
Arginase-1wogF02
F:29-298
1c
Arginase-1wogF03
F:29-298
1d
Arginase-1wogF04
F:29-298
1e
Arginase-1wogF05
F:29-298
1f
Arginase-1wogF06
F:29-298
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]
Atom Selection
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Asymmetric Unit 1
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