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3GN0
Asym. Unit
Info
Asym.Unit (110 KB)
Biol.Unit 1 (156 KB)
Biol.Unit 2 (156 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN ARGINASE I IN COMPLEX WITH DIFLUOROMETHYLORNITHINE (DFMO)
Authors
:
L. Di Costanzo, D. W. Christianson
Date
:
15 Mar 09 (Deposition) - 23 Feb 10 (Release) - 19 Jun 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.70
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (3x)
Biol. Unit 2: B (3x)
Keywords
:
Dfmo Binding, Polyamine Biosynthesis, Hydrolase-Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Ilies, L. Di Costanzo, D. P. Dowling, K. J. Thorn, D. W. Christianso
Binding Of Alpha, Alpha-Disubstituted Amino Acids To Arginas Suggests New Avenues For Inhibitor Design
J. Med. Chem. V. 54 5432 2011
[
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Hetero Components
(2, 6)
Info
All Hetero Components
1a: ALPHA-DIFLUOROMETHYLORNITHINE (DMOa)
1b: ALPHA-DIFLUOROMETHYLORNITHINE (DMOb)
2a: MANGANESE (II) ION (MNa)
2b: MANGANESE (II) ION (MNb)
2c: MANGANESE (II) ION (MNc)
2d: MANGANESE (II) ION (MNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DMO
2
Ligand/Ion
ALPHA-DIFLUOROMETHYLORNITHINE
2
MN
4
Ligand/Ion
MANGANESE (II) ION
[
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Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:124 , HIS A:126 , ASP A:232 , ASP A:234 , HOH A:437 , HOH A:438 , MN A:537
BINDING SITE FOR RESIDUE MN A 536
2
AC2
SOFTWARE
HIS A:101 , ASP A:124 , ASP A:128 , ASP A:232 , HOH A:435 , HOH A:437 , MN A:536
BINDING SITE FOR RESIDUE MN A 537
3
AC3
SOFTWARE
ASP A:128 , ASN A:130 , SER A:137 , HIS A:141 , GLY A:142 , ASP A:183 , GLU A:186 , HOH A:331 , HOH A:387 , HOH A:428 , HOH A:434 , HOH A:435 , HOH A:436 , HOH A:437 , HOH A:438 , HOH A:534
BINDING SITE FOR RESIDUE DMO A 551
4
AC4
SOFTWARE
ASP B:124 , HIS B:126 , ASP B:232 , ASP B:234 , HOH B:429 , MN B:537
BINDING SITE FOR RESIDUE MN B 536
5
AC5
SOFTWARE
HIS B:101 , ASP B:124 , ASP B:128 , ASP B:232 , HOH B:429 , HOH B:432 , MN B:536
BINDING SITE FOR RESIDUE MN B 537
6
AC6
SOFTWARE
HOH A:450 , ASP B:128 , ASN B:130 , SER B:137 , HIS B:141 , GLY B:142 , ASP B:183 , GLU B:186 , HOH B:350 , HOH B:429 , HOH B:430 , HOH B:431 , HOH B:432 , HOH B:538 , HOH B:539
BINDING SITE FOR RESIDUE DMO B 552
[
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SAPs(SNPs)/Variants
(10, 20)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_015594 (I11T, chain A/B, )
02: VAR_072164 (G27D, chain A/B, )
03: VAR_072165 (G74V, chain A/B, )
04: VAR_072166 (A125V, chain A/B, )
05: VAR_072167 (T134I, chain A/B, )
06: VAR_015595 (G138V, chain A/B, )
07: VAR_072168 (R180T, chain A/B, )
08: VAR_000674 (G235R, chain A/B, )
09: VAR_000675 (T290S, chain A/B, )
10: VAR_072169 (R308Q, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_015594
I
11
T
ARGI1_HUMAN
Disease (ARGIN)
28941474
A/B
I
11
T
02
UniProt
VAR_072164
G
27
D
ARGI1_HUMAN
Disease (ARGIN)
---
A/B
G
27
D
03
UniProt
VAR_072165
G
74
V
ARGI1_HUMAN
Disease (ARGIN)
---
A/B
G
74
V
04
UniProt
VAR_072166
A
125
V
ARGI1_HUMAN
Disease (ARGIN)
---
A/B
A
125
V
05
UniProt
VAR_072167
T
134
I
ARGI1_HUMAN
Disease (ARGIN)
---
A/B
T
134
I
06
UniProt
VAR_015595
G
138
V
ARGI1_HUMAN
Disease (ARGIN)
---
A/B
G
138
V
07
UniProt
VAR_072168
R
180
T
ARGI1_HUMAN
Disease (ARGIN)
---
A/B
R
180
T
08
UniProt
VAR_000674
G
235
R
ARGI1_HUMAN
Disease (ARGIN)
---
A/B
G
235
R
09
UniProt
VAR_000675
T
290
S
ARGI1_HUMAN
Polymorphism
---
A/B
T
290
S
10
UniProt
VAR_072169
R
308
Q
ARGI1_HUMAN
Disease (ARGIN)
---
A/B
R
308
Q
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: ARGINASE_1 (A:230-251,B:230-251)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ARGINASE_1
PS01053
Arginase family signature.
ARGI1_HUMAN
230-251
2
A:230-251
B:230-251
[
close PROSITE info
]
Exons
(8, 16)
Info
All Exons
Exon 1.1a (A:5-19 | B:5-19)
Exon 1.2b (A:20-44 | B:20-44)
Exon 1.3d (A:44-102 | B:44-102)
Exon 1.4c (A:102-155 | B:102-155)
Exon 1.5a (A:156-187 | B:156-187)
Exon 1.6b (A:187-222 | B:187-222)
Exon 1.7c (A:222-268 | B:222-268)
Exon 1.8b (A:268-319 | B:268-319)
View:
Select:
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All Exon Boundaries
1: Boundary -/1.1a
2: Boundary 1.1a/1.2b
3: Boundary 1.2b/1.3d
4: Boundary 1.3d/1.4c
5: Boundary 1.4c/1.5a
6: Boundary 1.5a/1.6b
7: Boundary 1.6b/1.7c
8: Boundary 1.7c/1.8b
9: Boundary 1.8b/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1a
ENST00000368087
1a
ENSE00001873351
chr6:
131894284-131894479
196
ARGI1_HUMAN
1-19
19
2
A:5-19
B:5-19
15
15
1.2b
ENST00000368087
2b
ENSE00002142788
chr6:
131897803-131897875
73
ARGI1_HUMAN
20-44
25
2
A:20-44
B:20-44
25
25
1.3d
ENST00000368087
3d
ENSE00002187903
chr6:
131900251-131900425
175
ARGI1_HUMAN
44-102
59
2
A:44-102
B:44-102
59
59
1.4c
ENST00000368087
4c
ENSE00002164252
chr6:
131902359-131902518
160
ARGI1_HUMAN
102-155
54
2
A:102-155
B:102-155
54
54
1.5a
ENST00000368087
5a
ENSE00002158516
chr6:
131903761-131903855
95
ARGI1_HUMAN
156-187
32
2
A:156-187
B:156-187
32
32
1.6b
ENST00000368087
6b
ENSE00002147839
chr6:
131904200-131904304
105
ARGI1_HUMAN
187-222
36
2
A:187-222
B:187-222
36
36
1.7c
ENST00000368087
7c
ENSE00000798683
chr6:
131904495-131904631
137
ARGI1_HUMAN
222-268
47
2
A:222-268
B:222-268
47
47
1.8b
ENST00000368087
8b
ENSE00001836591
chr6:
131904882-131905472
591
ARGI1_HUMAN
268-322
55
2
A:268-319
B:268-319
52
52
[
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]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d3gn0a_ (A:)
1b: SCOP_d3gn0b_ (B:)
View:
Select:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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
:
Arginase
(73)
Human (Homo sapiens) [TaxId: 9606]
(26)
1a
d3gn0a_
A:
1b
d3gn0b_
B:
[
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_3gn0A00 (A:5-319)
1b: CATH_3gn0B00 (B:5-319)
View:
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Classes
(
)
(
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)
(
)
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(
)
(
)
Homologous Superfamilies
(
)
(
)
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)
Human (Homo sapiens)
(15)
1a
3gn0A00
A:5-319
1b
3gn0B00
B:5-319
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
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(currently selected atoms:
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Nucleic
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Protein & NOT Site
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Chain B
Asymmetric Unit 1
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