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3MKV
Asym. Unit
Info
Asym.Unit (535 KB)
Biol.Unit 1 (526 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF AMIDOHYDROLASE EAJ56179
Authors
:
Y. Patskovsky, J. Bonanno, S. Ozyurt, J. M. Sauder, J. Freeman, B. Wu, D. K. Bain, L. Rodgers, S. R. Wasserman, F. M. Raushel, S. K. Burley, S. C. A York Sgx Research Center For Structural Genomics (Nysgxrc)
Date
:
15 Apr 10 (Deposition) - 28 Apr 10 (Release) - 02 Apr 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D,E,F,G,H (1x)
Keywords
:
Sargasso Sea, Structural Genomics, Protein Structure Initiative, Psi, New York Structural Genomix Research Consortium, Nysgxrc, Prolidase, Hydrolase, New York Sgx Research Center For Structural Genomics
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. F. Xiang, Y. Patskovsky, C. Xu, A. A. Fedorov, E. V. Fedorov, A. A. Sisco, J. M. Sauder, S. K. Burley, S. C. Almo, F. M. Raushel
Functional Identification And Structure Determination Of Tw Novel Prolidases From Cog1228 In The Amidohydrolase Superfamily .
Biochemistry V. 49 6791 2010
[
close entry info
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Hetero Components
(5, 41)
Info
All Hetero Components
1a: CARBONATE ION (CO3a)
1b: CARBONATE ION (CO3b)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
3a: LYSINE NZ-CARBOXYLIC ACID (KCXa)
3b: LYSINE NZ-CARBOXYLIC ACID (KCXb)
3c: LYSINE NZ-CARBOXYLIC ACID (KCXc)
3d: LYSINE NZ-CARBOXYLIC ACID (KCXd)
3e: LYSINE NZ-CARBOXYLIC ACID (KCXe)
3f: LYSINE NZ-CARBOXYLIC ACID (KCXf)
3g: LYSINE NZ-CARBOXYLIC ACID (KCXg)
3h: LYSINE NZ-CARBOXYLIC ACID (KCXh)
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)
5a: ZINC ION (ZNa)
5b: ZINC ION (ZNb)
5c: ZINC ION (ZNc)
5d: ZINC ION (ZNd)
5e: ZINC ION (ZNe)
5f: ZINC ION (ZNf)
5g: ZINC ION (ZNg)
5h: ZINC ION (ZNh)
5i: ZINC ION (ZNi)
5j: ZINC ION (ZNj)
5k: ZINC ION (ZNk)
5l: ZINC ION (ZNl)
5m: ZINC ION (ZNm)
5n: ZINC ION (ZNn)
5o: ZINC ION (ZNo)
5p: ZINC ION (ZNp)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CO3
2
Ligand/Ion
CARBONATE ION
2
GOL
2
Ligand/Ion
GLYCEROL
3
KCX
8
Mod. Amino Acid
LYSINE NZ-CARBOXYLIC ACID
4
SO4
13
Ligand/Ion
SULFATE ION
5
ZN
16
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(33, 33)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:63 , HIS A:65 , KCX A:191 , ASP A:324 , ZN A:426
BINDING SITE FOR RESIDUE ZN A 425
02
AC2
SOFTWARE
KCX A:191 , HIS A:232 , HIS A:252 , ZN A:425 , SO4 A:427
BINDING SITE FOR RESIDUE ZN A 426
03
AC3
SOFTWARE
HIS A:140 , GLY A:197 , VAL A:198 , ALA A:199 , HIS A:232 , TYR A:234 , ZN A:426 , HOH A:435 , HOH A:558
BINDING SITE FOR RESIDUE SO4 A 427
04
AC4
SOFTWARE
ARG A:248 , TYR A:270 , LYS A:318
BINDING SITE FOR RESIDUE SO4 A 428
05
AC5
SOFTWARE
HIS B:63 , HIS B:65 , KCX B:191 , ASP B:324 , ZN B:426 , HOH B:546
BINDING SITE FOR RESIDUE ZN B 425
06
AC6
SOFTWARE
KCX B:191 , HIS B:232 , HIS B:252 , ZN B:425 , SO4 B:427 , HOH B:546
BINDING SITE FOR RESIDUE ZN B 426
07
AC7
SOFTWARE
HIS B:140 , GLY B:197 , VAL B:198 , ALA B:199 , HIS B:232 , TYR B:234 , ZN B:426 , HOH B:513 , HOH B:546
BINDING SITE FOR RESIDUE SO4 B 427
08
AC8
SOFTWARE
ARG B:248 , GLY B:268 , TYR B:270 , LYS B:318
BINDING SITE FOR RESIDUE SO4 B 428
09
AC9
SOFTWARE
HIS C:63 , HIS C:65 , KCX C:191 , ASP C:324 , ZN C:426
BINDING SITE FOR RESIDUE ZN C 425
10
BC1
SOFTWARE
KCX C:191 , HIS C:232 , HIS C:252 , ZN C:425 , SO4 C:427 , HOH C:557
BINDING SITE FOR RESIDUE ZN C 426
11
BC2
SOFTWARE
HIS C:140 , GLY C:197 , VAL C:198 , ALA C:199 , HIS C:232 , TYR C:234 , ZN C:426 , HOH C:557
BINDING SITE FOR RESIDUE SO4 C 427
12
BC3
SOFTWARE
LEU C:73 , ALA C:141 , ALA C:164 , LEU C:165 , GLY C:166 , HOH C:542 , HOH C:561
BINDING SITE FOR RESIDUE GOL C 428
13
BC4
SOFTWARE
HIS D:63 , HIS D:65 , KCX D:191 , ASP D:324 , ZN D:426
BINDING SITE FOR RESIDUE ZN D 425
14
BC5
SOFTWARE
KCX D:191 , HIS D:232 , HIS D:252 , ZN D:425
BINDING SITE FOR RESIDUE ZN D 426
15
BC6
SOFTWARE
ARG D:248 , GLY D:268 , TYR D:270 , LYS D:318
BINDING SITE FOR RESIDUE SO4 D 427
16
BC7
SOFTWARE
ARG D:244 , GLU D:266 , HIS D:267 , LYS F:318
BINDING SITE FOR RESIDUE SO4 D 428
17
BC8
SOFTWARE
LEU D:73 , ALA D:77 , ALA D:141 , GLY D:163 , LEU D:165 , GLY D:166 , HOH D:455
BINDING SITE FOR RESIDUE GOL D 429
18
BC9
SOFTWARE
HIS E:63 , HIS E:65 , KCX E:191 , ASP E:324 , ZN E:426
BINDING SITE FOR RESIDUE ZN E 425
19
CC1
SOFTWARE
KCX E:191 , HIS E:232 , HIS E:252 , ZN E:425 , SO4 E:428
BINDING SITE FOR RESIDUE ZN E 426
20
CC2
SOFTWARE
ARG E:248 , GLY E:268 , TYR E:270 , LYS E:318
BINDING SITE FOR RESIDUE SO4 E 427
21
CC3
SOFTWARE
HIS E:140 , VAL E:198 , ALA E:199 , HIS E:232 , TYR E:234 , ZN E:426 , HOH E:489
BINDING SITE FOR RESIDUE SO4 E 428
22
CC4
SOFTWARE
HIS F:63 , HIS F:65 , KCX F:191 , ASP F:324 , ZN F:426
BINDING SITE FOR RESIDUE ZN F 425
23
CC5
SOFTWARE
KCX F:191 , HIS F:232 , HIS F:252 , ZN F:425 , HOH F:494
BINDING SITE FOR RESIDUE ZN F 426
24
CC6
SOFTWARE
HIS F:140 , VAL F:198 , ALA F:199 , TYR F:234 , ASP F:324 , HOH F:494 , HOH F:501
BINDING SITE FOR RESIDUE CO3 F 427
25
CC7
SOFTWARE
HIS G:63 , HIS G:65 , KCX G:191 , ASP G:324 , ZN G:426
BINDING SITE FOR RESIDUE ZN G 425
26
CC8
SOFTWARE
KCX G:191 , HIS G:232 , HIS G:252 , ZN G:425 , HOH G:554
BINDING SITE FOR RESIDUE ZN G 426
27
CC9
SOFTWARE
ARG G:248 , GLY G:268 , TYR G:270 , LYS G:318
BINDING SITE FOR RESIDUE SO4 G 427
28
DC1
SOFTWARE
HIS G:140 , VAL G:198 , ALA G:199 , HIS G:232 , TYR G:234 , ASP G:324
BINDING SITE FOR RESIDUE CO3 G 428
29
DC2
SOFTWARE
HIS H:63 , HIS H:65 , KCX H:191 , ASP H:324 , ZN H:426 , HOH H:496
BINDING SITE FOR RESIDUE ZN H 425
30
DC3
SOFTWARE
KCX H:191 , HIS H:232 , HIS H:252 , ZN H:425 , SO4 H:427 , HOH H:496
BINDING SITE FOR RESIDUE ZN H 426
31
DC4
SOFTWARE
HIS H:140 , GLY H:197 , VAL H:198 , ALA H:199 , HIS H:232 , TYR H:234 , HIS H:252 , ZN H:426 , HOH H:496 , HOH H:502
BINDING SITE FOR RESIDUE SO4 H 427
32
DC5
SOFTWARE
ARG H:248 , TYR H:270 , LYS H:318
BINDING SITE FOR RESIDUE SO4 H 428
33
DC6
SOFTWARE
ARG H:244 , LEU H:263 , GLU H:266 , HIS H:267
BINDING SITE FOR RESIDUE SO4 H 429
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
End label:
Sorry, no Info available
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 16)
Info
All SCOP Domains
1a: SCOP_d3mkva1 (A:1-57,A:369-414)
1b: SCOP_d3mkvb1 (B:2-57,B:369-414)
1c: SCOP_d3mkvc1 (C:2-57,C:369-414)
1d: SCOP_d3mkvd1 (D:2-57,D:369-414)
1e: SCOP_d3mkve1 (E:2-57,E:369-414)
1f: SCOP_d3mkvf1 (F:2-57,F:369-414)
1g: SCOP_d3mkvg1 (G:2-57,G:369-414)
1h: SCOP_d3mkvh1 (H:2-57,H:369-414)
2a: SCOP_d3mkva2 (A:58-368)
2b: SCOP_d3mkvb2 (B:58-368)
2c: SCOP_d3mkvc2 (C:58-368)
2d: SCOP_d3mkvd2 (D:58-368)
2e: SCOP_d3mkve2 (E:58-368)
2f: SCOP_d3mkvf2 (F:58-368)
2g: SCOP_d3mkvg2 (G:58-368)
2h: SCOP_d3mkvh2 (H:58-368)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Composite domain of metallo-dependent hydrolases
(103)
Superfamily
:
Composite domain of metallo-dependent hydrolases
(103)
Family
:
Zn-dependent arginine carboxypeptidase-like
(4)
Protein domain
:
Uncharacterized protein EAJ56179
(1)
Unidentified organism [TaxId: 32644]
(1)
1a
d3mkva1
A:1-57,A:369-414
1b
d3mkvb1
B:2-57,B:369-414
1c
d3mkvc1
C:2-57,C:369-414
1d
d3mkvd1
D:2-57,D:369-414
1e
d3mkve1
E:2-57,E:369-414
1f
d3mkvf1
F:2-57,F:369-414
1g
d3mkvg1
G:2-57,G:369-414
1h
d3mkvh1
H:2-57,H:369-414
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Metallo-dependent hydrolases
(273)
Family
:
Zn-dependent arginine carboxypeptidase-like
(4)
Protein domain
:
Uncharacterized protein EAJ56179
(1)
Unidentified organism [TaxId: 32644]
(1)
2a
d3mkva2
A:58-368
2b
d3mkvb2
B:58-368
2c
d3mkvc2
C:58-368
2d
d3mkvd2
D:58-368
2e
d3mkve2
E:58-368
2f
d3mkvf2
F:58-368
2g
d3mkvg2
G:58-368
2h
d3mkvh2
H:58-368
[
close SCOP info
]
CATH Domains
(0, 0 ; only for superseded entry 2R8C: 2,16)
Info
all CATH domains
1a: CATH_2r8cA02 ()
1b: CATH_2r8cE02 ()
1c: CATH_2r8cG02 ()
1d: CATH_2r8cD02 ()
1e: CATH_2r8cH02 ()
1f: CATH_2r8cB02 ()
1g: CATH_2r8cF02 ()
1h: CATH_2r8cC02 ()
2a: CATH_2r8cA01 ()
2b: CATH_2r8cC01 ()
2c: CATH_2r8cD01 ()
2d: CATH_2r8cE01 ()
2e: CATH_2r8cF01 ()
2f: CATH_2r8cG01 ()
2g: CATH_2r8cH01 ()
2h: CATH_2r8cB01 ()
View:
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Sorry, no Info available
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Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Sorry, no Info available
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