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1PQ3
Asym. Unit
Info
Asym.Unit (302 KB)
Biol.Unit 1 (151 KB)
Biol.Unit 2 (150 KB)
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(1)
Title
:
HUMAN ARGINASE II: CRYSTAL STRUCTURE AND PHYSIOLOGICAL ROLE IN MALE AND FEMALE SEXUAL AROUSAL
Authors
:
E. Cama, D. M. Colleluori, F. A. Emig, H. Shin, S. W. Kim, N. N. Kim, A. M. Tr D. E. Ash, D. W. Christianson
Date
:
17 Jun 03 (Deposition) - 12 Aug 03 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C (1x)
Biol. Unit 2: D,E,F (1x)
Keywords
:
Biosynthetic Protein, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. Cama, D. M. Colleluori, F. A. Emig, H. Shin, S. W. Kim, N. N. Kim, A. M. Traish, D. E. Ash, D. W. Christianson
Human Arginase Ii: Crystal Structure And Physiological Role In Male And Female Sexual Arousal
Biochemistry V. 42 8445 2003
[
close entry info
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Hetero Components
(4, 38)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
1d: CHLORIDE ION (CLd)
1e: CHLORIDE ION (CLe)
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)
3a: S-2-(BORONOETHYL)-L-CYSTEINE (S2Ca)
3b: S-2-(BORONOETHYL)-L-CYSTEINE (S2Cb)
3c: S-2-(BORONOETHYL)-L-CYSTEINE (S2Cc)
3d: S-2-(BORONOETHYL)-L-CYSTEINE (S2Cd)
3e: S-2-(BORONOETHYL)-L-CYSTEINE (S2Ce)
3f: S-2-(BORONOETHYL)-L-CYSTEINE (S2Cf)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
4e: SULFATE ION (SO4e)
4f: SULFATE ION (SO4f)
4g: SULFATE ION (SO4g)
4h: SULFATE ION (SO4h)
4i: SULFATE ION (SO4i)
4j: SULFATE ION (SO4j)
4k: SULFATE ION (SO4k)
4l: SULFATE ION (SO4l)
4m: SULFATE ION (SO4m)
4n: SULFATE ION (SO4n)
4o: SULFATE ION (SO4o)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
5
Ligand/Ion
CHLORIDE ION
2
MN
12
Ligand/Ion
MANGANESE (II) ION
3
S2C
6
Ligand/Ion
S-2-(BORONOETHYL)-L-CYSTEINE
4
SO4
15
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(37, 37)
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)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:220 , ARG A:224
BINDING SITE FOR RESIDUE SO4 A 3070
02
AC2
SOFTWARE
ARG F:220 , ASP F:221 , ARG F:224 , HOH F:973
BINDING SITE FOR RESIDUE SO4 F 3071
03
AC3
SOFTWARE
ARG D:220 , ARG D:224
BINDING SITE FOR RESIDUE SO4 D 3072
04
AC4
SOFTWARE
ARG A:224 , ARG A:233
BINDING SITE FOR RESIDUE SO4 A 3073
05
AC5
SOFTWARE
ARG F:224 , LEU F:225 , ARG F:233
BINDING SITE FOR RESIDUE SO4 F 3074
06
AC6
SOFTWARE
ARG C:220 , ARG C:224
BINDING SITE FOR RESIDUE SO4 C 3075
07
AC7
SOFTWARE
PRO F:179 , GLY F:180 , PHE F:181 , SER F:182
BINDING SITE FOR RESIDUE SO4 F 3077
08
AC8
SOFTWARE
PRO C:179 , GLY C:180 , PHE C:181 , SER C:182
BINDING SITE FOR RESIDUE SO4 C 3078
09
AC9
SOFTWARE
GLY D:180 , PHE D:181 , SER D:182
BINDING SITE FOR RESIDUE SO4 D 3079
10
BC1
SOFTWARE
ARG D:90 , PRO D:179
BINDING SITE FOR RESIDUE SO4 D 3080
11
BC2
SOFTWARE
ARG A:90 , PRO A:179
BINDING SITE FOR RESIDUE SO4 A 3081
12
BC3
SOFTWARE
GLY A:180 , PHE A:181 , SER A:182
BINDING SITE FOR RESIDUE SO4 A 3082
13
BC4
SOFTWARE
ARG D:224 , ARG D:233 , HOH D:1050
BINDING SITE FOR RESIDUE SO4 D 3083
14
BC5
SOFTWARE
LYS F:241 , ARG F:242 , ARG F:244 , HOH F:1175
BINDING SITE FOR RESIDUE SO4 F 3084
15
BC6
SOFTWARE
SER B:189 , SER B:192 , ARG B:242 , ARG B:244
BINDING SITE FOR RESIDUE SO4 B 3085
16
BC7
SOFTWARE
HIS A:120 , ASP A:143 , ASP A:147 , ASP A:251 , MN A:501 , S2C A:551
BINDING SITE FOR RESIDUE MN A 500
17
BC8
SOFTWARE
ASP A:143 , HIS A:145 , ASP A:251 , ASP A:253 , MN A:500 , S2C A:551
BINDING SITE FOR RESIDUE MN A 501
18
BC9
SOFTWARE
HIS B:120 , ASP B:143 , ASP B:147 , ASP B:251 , MN B:503 , S2C B:552
BINDING SITE FOR RESIDUE MN B 502
19
CC1
SOFTWARE
ASP B:143 , HIS B:145 , ASP B:251 , ASP B:253 , MN B:502 , S2C B:552
BINDING SITE FOR RESIDUE MN B 503
20
CC2
SOFTWARE
ASP C:143 , HIS C:145 , ASP C:251 , ASP C:253 , MN C:505 , S2C C:553
BINDING SITE FOR RESIDUE MN C 504
21
CC3
SOFTWARE
HIS C:120 , ASP C:143 , ASP C:147 , ASP C:251 , MN C:504 , S2C C:553
BINDING SITE FOR RESIDUE MN C 505
22
CC4
SOFTWARE
HIS D:120 , ASP D:143 , ASP D:147 , ASP D:251 , MN D:507 , S2C D:554
BINDING SITE FOR RESIDUE MN D 506
23
CC5
SOFTWARE
ASP D:143 , HIS D:145 , ASP D:251 , ASP D:253 , MN D:506 , S2C D:554
BINDING SITE FOR RESIDUE MN D 507
24
CC6
SOFTWARE
HIS E:120 , ASP E:143 , ASP E:147 , ASP E:251 , MN E:509 , S2C E:555
BINDING SITE FOR RESIDUE MN E 508
25
CC7
SOFTWARE
ASP E:143 , HIS E:145 , ASP E:251 , ASP E:253 , MN E:508 , S2C E:555
BINDING SITE FOR RESIDUE MN E 509
26
CC8
SOFTWARE
ASP F:143 , HIS F:145 , ASP F:251 , ASP F:253 , MN F:511 , S2C F:556
BINDING SITE FOR RESIDUE MN F 510
27
CC9
SOFTWARE
HIS F:120 , ASP F:143 , ASP F:147 , ASP F:251 , MN F:510 , S2C F:556
BINDING SITE FOR RESIDUE MN F 511
28
DC1
SOFTWARE
ARG E:242
BINDING SITE FOR RESIDUE CL E 600
29
DC2
SOFTWARE
ARG C:50 , GLU C:51 , GLY C:53 , HOH C:939
BINDING SITE FOR RESIDUE CL A 601
30
DC3
SOFTWARE
GLN C:243
BINDING SITE FOR RESIDUE CL C 602
31
DC4
SOFTWARE
GLN F:243
BINDING SITE FOR RESIDUE CL F 605
32
DC5
SOFTWARE
HIS A:120 , ASP A:143 , HIS A:145 , ASP A:147 , ASN A:149 , SER A:156 , HIS A:160 , GLY A:161 , ASP A:202 , ASP A:251 , ASP A:253 , GLU A:296 , MN A:500 , MN A:501 , HOH A:917 , HOH A:918 , HOH A:925 , HOH A:1076 , HOH A:1205
BINDING SITE FOR RESIDUE S2C A 551
33
DC6
SOFTWARE
HIS B:120 , ASP B:143 , HIS B:145 , ASP B:147 , ASN B:149 , SER B:156 , HIS B:160 , GLY B:161 , ASP B:202 , ASP B:251 , ASP B:253 , THR B:265 , GLU B:296 , MN B:502 , MN B:503 , HOH B:920 , HOH B:921 , HOH B:999
BINDING SITE FOR RESIDUE S2C B 552
34
DC7
SOFTWARE
HIS C:120 , ASP C:143 , HIS C:145 , ASP C:147 , ASN C:149 , THR C:154 , SER C:156 , HIS C:160 , ASP C:202 , ASP C:251 , ASP C:253 , THR C:265 , GLU C:296 , MN C:504 , MN C:505 , HOH C:922 , HOH C:923 , HOH C:1077 , HOH C:1147
BINDING SITE FOR RESIDUE S2C C 553
35
DC8
SOFTWARE
HIS D:120 , ASP D:143 , HIS D:145 , ASP D:147 , ASN D:149 , SER D:156 , HIS D:160 , GLY D:161 , ASP D:202 , ASP D:251 , ASP D:253 , GLU D:296 , MN D:506 , MN D:507 , HOH D:924 , HOH D:926 , HOH D:927 , HOH D:1078
BINDING SITE FOR RESIDUE S2C D 554
36
DC9
SOFTWARE
HIS E:120 , ASP E:143 , HIS E:145 , ASP E:147 , ASN E:149 , SER E:156 , HIS E:160 , GLY E:161 , ASP E:202 , ASP E:251 , ASP E:253 , THR E:265 , GLU E:296 , MN E:508 , MN E:509 , HOH E:931 , HOH E:932 , HOH E:933 , HOH E:1053 , HOH E:1056
BINDING SITE FOR RESIDUE S2C E 555
37
EC1
SOFTWARE
HIS F:120 , ASP F:143 , HIS F:145 , ASP F:147 , ASN F:149 , SER F:156 , HIS F:160 , ASP F:202 , ASP F:251 , ASP F:253 , THR F:265 , GLU F:296 , MN F:510 , MN F:511 , HOH F:928 , HOH F:929 , HOH F:930 , HOH F:1054 , HOH F:1148
BINDING SITE FOR RESIDUE S2C F 556
[
close Site info
]
SAPs(SNPs)/Variants
(1, 6)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_033520 (G240R, chain A/B/C/D/E/F, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_033520
G
240
R
ARGI2_HUMAN
Polymorphism
17104534
A/B/C/D/E/F
G
240
R
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 6)
Info
All PROSITE Patterns/Profiles
1: ARGINASE_1 (A:249-270,B:249-270,C:249-270,D:24...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ARGINASE_1
PS01053
Arginase family signature.
ARGI2_HUMAN
249-270
6
A:249-270
B:249-270
C:249-270
D:249-270
E:249-270
F:249-270
[
close PROSITE info
]
Exons
(8, 48)
Info
All Exons
Exon 1.1 (A:24-37 | B:24-37 | C:24-37 | D:24...)
Exon 1.2 (A:38-62 | B:38-62 | C:38-62 | D:38...)
Exon 1.3 (A:62-121 | B:62-121 | C:62-121 | D...)
Exon 1.4 (A:121-174 | B:121-174 | C:121-174 ...)
Exon 1.5 (A:175-206 | B:175-206 | C:175-206 ...)
Exon 1.6 (A:206-241 | B:206-241 | C:206-241 ...)
Exon 1.7 (A:241-287 | B:241-287 | C:241-287 ...)
Exon 1.8 (A:287-329 | B:287-329 | C:287-329 ...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/1.2
3: Boundary 1.2/1.3
4: Boundary 1.3/1.4
5: Boundary 1.4/1.5
6: Boundary 1.5/1.6
7: Boundary 1.6/1.7
8: Boundary 1.7/1.8
9: Boundary 1.8/-
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
1.1
ENST00000261783
1
ENSE00001168252
chr14:
68086579-68086805
227
ARGI2_HUMAN
1-37
37
6
A:24-37
B:24-37
C:24-37
D:24-37
E:24-37
F:24-37
14
14
14
14
14
14
1.2
ENST00000261783
2
ENSE00000522767
chr14:
68087611-68087683
73
ARGI2_HUMAN
38-62
25
6
A:38-62
B:38-62
C:38-62
D:38-62
E:38-62
F:38-62
25
25
25
25
25
25
1.3
ENST00000261783
3
ENSE00000940940
chr14:
68108903-68109080
178
ARGI2_HUMAN
62-121
60
6
A:62-121
B:62-121
C:62-121
D:62-121
E:62-121
F:62-121
60
60
60
60
60
60
1.4
ENST00000261783
4
ENSE00000658651
chr14:
68112360-68112519
160
ARGI2_HUMAN
121-174
54
6
A:121-174
B:121-174
C:121-174
D:121-174
E:121-174
F:121-174
54
54
54
54
54
54
1.5
ENST00000261783
5
ENSE00000658652
chr14:
68113361-68113455
95
ARGI2_HUMAN
175-206
32
6
A:175-206
B:175-206
C:175-206
D:175-206
E:175-206
F:175-206
32
32
32
32
32
32
1.6
ENST00000261783
6
ENSE00000658653
chr14:
68113638-68113742
105
ARGI2_HUMAN
206-241
36
6
A:206-241
B:206-241
C:206-241
D:206-241
E:206-241
F:206-241
36
36
36
36
36
36
1.7
ENST00000261783
7
ENSE00000658654
chr14:
68114764-68114900
137
ARGI2_HUMAN
241-287
47
6
A:241-287
B:241-287
C:241-287
D:241-287
E:241-287
F:241-287
47
47
47
47
47
47
1.8
ENST00000261783
8
ENSE00001168242
chr14:
68117432-68118437
1006
ARGI2_HUMAN
287-354
68
6
A:287-329
B:287-329
C:287-329
D:287-329
E:287-329
F:287-329
43
43
43
43
43
43
[
close EXON info
]
SCOP Domains
(1, 6)
Info
All SCOP Domains
1a: SCOP_d1pq3a_ (A:)
1b: SCOP_d1pq3b_ (B:)
1c: SCOP_d1pq3c_ (C:)
1d: SCOP_d1pq3d_ (D:)
1e: SCOP_d1pq3e_ (E:)
1f: SCOP_d1pq3f_ (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
:
Arginase
(73)
Human (Homo sapiens), isoform II, mitochondrial [TaxId: 9606]
(7)
1a
d1pq3a_
A:
1b
d1pq3b_
B:
1c
d1pq3c_
C:
1d
d1pq3d_
D:
1e
d1pq3e_
E:
1f
d1pq3f_
F:
[
close SCOP info
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CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_1pq3A00 (A:24-329)
1b: CATH_1pq3B00 (B:24-329)
1c: CATH_1pq3C00 (C:24-329)
1d: CATH_1pq3D00 (D:24-329)
1e: CATH_1pq3E00 (E:24-329)
1f: CATH_1pq3F00 (F:24-329)
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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)
Human (Homo sapiens)
(15)
1a
1pq3A00
A:24-329
1b
1pq3B00
B:24-329
1c
1pq3C00
C:24-329
1d
1pq3D00
D:24-329
1e
1pq3E00
E:24-329
1f
1pq3F00
F:24-329
[
close CATH info
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Pfam Domains
(1, 6)
Info
all PFAM domains
1a: PFAM_Arginase_1pq3F01 (F:24-324)
1b: PFAM_Arginase_1pq3F02 (F:24-324)
1c: PFAM_Arginase_1pq3F03 (F:24-324)
1d: PFAM_Arginase_1pq3F04 (F:24-324)
1e: PFAM_Arginase_1pq3F05 (F:24-324)
1f: PFAM_Arginase_1pq3F06 (F:24-324)
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Organisms
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Clan
:
Arginase
(56)
Family
:
Arginase
(37)
Homo sapiens (Human)
(11)
1a
Arginase-1pq3F01
F:24-324
1b
Arginase-1pq3F02
F:24-324
1c
Arginase-1pq3F03
F:24-324
1d
Arginase-1pq3F04
F:24-324
1e
Arginase-1pq3F05
F:24-324
1f
Arginase-1pq3F06
F:24-324
[
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Atom Selection
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Chain F
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select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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show SS bonds with a radius of 100 units (=0.4Å)
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Asym.Unit (302 KB)
Header - Asym.Unit
Biol.Unit 1 (151 KB)
Header - Biol.Unit 1
Biol.Unit 2 (150 KB)
Header - Biol.Unit 2
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