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3HK7
Biol. Unit 4
Info
Asym.Unit (868 KB)
Biol.Unit 1 (506 KB)
Biol.Unit 2 (577 KB)
Biol.Unit 3 (647 KB)
Biol.Unit 4 (508 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF URONATE ISOMERASE FROM BACILLUS HALODURANS COMPLEXED WITH ZINC AND D-ARABINARATE, MONOCLINIC CRYSTAL FORM
Authors
:
A. A. Fedorov, E. V. Fedorov, T. T. Nguyen, F. M. Raushel, S. C. Almo
Date
:
22 May 09 (Deposition) - 25 Aug 09 (Release) - 29 Sep 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,C,D,G,H,K (1x)
Biol. Unit 2: A,B,D,E,F,H,J,L (1x)
Biol. Unit 3: B,C,E,F,G,H,I,K,L (1x)
Biol. Unit 4: C,D,F,G,J,K,L (1x)
Keywords
:
Uronate Isomerase, Mechanism Of The Reaction, D-Arabinarate
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. T. Nguyen, A. A. Fedorov, L. Williams, E. V. Fedorov, Y. Li, C. Xu, S. C. Almo, F. M. Raushel
The Mechanism Of The Reaction Catalyzed By Uronate Isomerase Illustrates How An Isomerase May Have Evolved From A Hydrolase Within The Amidohydrolase Superfamily.
Biochemistry V. 48 8879 2009
(for further references see the
PDB file header
)
[
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Hetero Components
(2, 13)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
1d: CHLORIDE ION (CLd)
2a: CARBONATE ION (CO3a)
2b: CARBONATE ION (CO3b)
2c: CARBONATE ION (CO3c)
2d: CARBONATE ION (CO3d)
2e: CARBONATE ION (CO3e)
2f: CARBONATE ION (CO3f)
2g: CARBONATE ION (CO3g)
2h: CARBONATE ION (CO3h)
2i: CARBONATE ION (CO3i)
2j: CARBONATE ION (CO3j)
2k: CARBONATE ION (CO3k)
2l: CARBONATE ION (CO3l)
3a: SODIUM ION (NAa)
3b: SODIUM ION (NAb)
3c: SODIUM ION (NAc)
3d: SODIUM ION (NAd)
4a: D-ARABINARIC ACID (RATa)
4b: D-ARABINARIC ACID (RATb)
4c: D-ARABINARIC ACID (RATc)
4d: D-ARABINARIC ACID (RATd)
4e: D-ARABINARIC ACID (RATe)
4f: D-ARABINARIC ACID (RATf)
4g: D-ARABINARIC ACID (RATg)
4h: D-ARABINARIC ACID (RATh)
4i: D-ARABINARIC ACID (RATi)
4j: D-ARABINARIC ACID (RATj)
4k: D-ARABINARIC ACID (RATk)
4l: D-ARABINARIC ACID (RATl)
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)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
-1
Ligand/Ion
CHLORIDE ION
2
CO3
6
Ligand/Ion
CARBONATE ION
3
NA
-1
Ligand/Ion
SODIUM ION
4
RAT
7
Ligand/Ion
D-ARABINARIC ACID
5
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(32, 32)
Info
All Sites
01: AC3 (SOFTWARE)
02: AC5 (SOFTWARE)
03: AC8 (SOFTWARE)
04: AC9 (SOFTWARE)
05: BC1 (SOFTWARE)
06: BC2 (SOFTWARE)
07: BC3 (SOFTWARE)
08: BC4 (SOFTWARE)
09: BC5 (SOFTWARE)
10: BC6 (SOFTWARE)
11: BC8 (SOFTWARE)
12: BC9 (SOFTWARE)
13: CC2 (SOFTWARE)
14: CC3 (SOFTWARE)
15: CC4 (SOFTWARE)
16: CC5 (SOFTWARE)
17: CC6 (SOFTWARE)
18: CC7 (SOFTWARE)
19: CC8 (SOFTWARE)
20: DC1 (SOFTWARE)
21: DC3 (SOFTWARE)
22: DC7 (SOFTWARE)
23: DC8 (SOFTWARE)
24: DC9 (SOFTWARE)
25: EC1 (SOFTWARE)
26: EC2 (SOFTWARE)
27: EC3 (SOFTWARE)
28: EC4 (SOFTWARE)
29: EC5 (SOFTWARE)
30: EC6 (SOFTWARE)
31: EC7 (SOFTWARE)
32: EC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC3
SOFTWARE
ARG A:314 , LYS A:315 , HIS C:49 , TYR C:50 , TRP C:326 , PHE C:327 , HOH C:1835
BINDING SITE FOR RESIDUE CO3 A 430
02
AC5
SOFTWARE
HOH A:433 , HOH A:881 , HOH B:433 , HOH B:1378 , HOH C:466 , HOH C:1634
BINDING SITE FOR RESIDUE NA A 432
03
AC8
SOFTWARE
LYS A:278 , GLU A:304 , LYS B:278 , GLU B:304 , LYS C:278 , GLU C:304
BINDING SITE FOR RESIDUE CL B 430
04
AC9
SOFTWARE
HIS C:26 , HIS C:28 , HIS C:49 , TYR C:50 , ARG C:170 , MET C:258 , TRP C:325 , TRP C:326 , ASP C:355 , ARG C:357 , ZN C:430 , HOH C:542 , HOH C:967 , HOH C:1392 , HOH C:1849
BINDING SITE FOR RESIDUE RAT C 428
05
BC1
SOFTWARE
HIS B:49 , TYR B:50 , TRP B:326 , PHE B:327 , HOH B:1834 , ARG C:314 , LYS C:315
BINDING SITE FOR RESIDUE CO3 C 429
06
BC2
SOFTWARE
HIS C:26 , HIS C:28 , ASP C:355 , RAT C:428
BINDING SITE FOR RESIDUE ZN C 430
07
BC3
SOFTWARE
HIS D:26 , HIS D:28 , HIS D:49 , TYR D:50 , ARG D:170 , MET D:258 , TRP D:325 , TRP D:326 , ASP D:355 , ARG D:357 , ZN D:430 , HOH D:439 , HOH D:445 , HOH D:505
BINDING SITE FOR RESIDUE RAT D 428
08
BC4
SOFTWARE
ARG D:314 , LYS D:315 , HIS F:49 , TYR F:50 , TRP F:326 , PHE F:327 , HOH F:1838
BINDING SITE FOR RESIDUE CO3 D 429
09
BC5
SOFTWARE
HIS D:26 , HIS D:28 , ASP D:355 , RAT D:428
BINDING SITE FOR RESIDUE ZN D 430
10
BC6
SOFTWARE
HOH D:823 , HOH D:1832 , HOH E:651 , HOH E:1613 , HOH F:450 , HOH F:683
BINDING SITE FOR RESIDUE NA D 431
11
BC8
SOFTWARE
HIS D:49 , TYR D:50 , ALA D:53 , TRP D:326 , PHE D:327 , ARG E:314 , LYS E:315 , HOH E:1836
BINDING SITE FOR RESIDUE CO3 E 429
12
BC9
SOFTWARE
HIS E:49 , TYR E:50 , TRP E:326 , PHE E:327 , HOH E:1837 , ARG F:314 , LYS F:315
BINDING SITE FOR RESIDUE CO3 E 430
13
CC2
SOFTWARE
LYS D:278 , GLU D:304 , LYS E:278 , GLU E:304 , LYS F:278 , GLU F:304
BINDING SITE FOR RESIDUE CL E 432
14
CC3
SOFTWARE
HIS F:26 , HIS F:28 , HIS F:49 , TYR F:50 , ARG F:170 , MET F:258 , TRP F:325 , TRP F:326 , ASP F:355 , ARG F:357 , ZN F:429 , HOH F:745 , HOH F:1201 , HOH F:1401 , HOH F:1857
BINDING SITE FOR RESIDUE RAT F 428
15
CC4
SOFTWARE
HIS F:26 , HIS F:28 , ASP F:355 , RAT F:428
BINDING SITE FOR RESIDUE ZN F 429
16
CC5
SOFTWARE
HIS G:26 , HIS G:28 , HIS G:49 , TYR G:50 , ARG G:170 , SER G:223 , MET G:258 , TRP G:325 , TRP G:326 , ASP G:355 , ARG G:357 , ZN G:430 , HOH G:751 , HOH G:1456
BINDING SITE FOR RESIDUE RAT G 428
17
CC6
SOFTWARE
ARG G:314 , LYS G:315 , HIS I:49 , TYR I:50 , ALA I:53 , TRP I:326 , PHE I:327 , HOH I:1841
BINDING SITE FOR RESIDUE CO3 G 429
18
CC7
SOFTWARE
HIS G:26 , HIS G:28 , ASP G:355 , RAT G:428
BINDING SITE FOR RESIDUE ZN G 430
19
CC8
SOFTWARE
LYS G:278 , GLU G:304 , LYS H:278 , GLU H:304 , LYS I:278 , GLU I:304
BINDING SITE FOR RESIDUE CL G 431
20
DC1
SOFTWARE
HIS G:49 , TYR G:50 , ALA G:53 , TRP G:326 , PHE G:327 , HOH G:1839 , ARG H:314 , LYS H:315
BINDING SITE FOR RESIDUE CO3 H 429
21
DC3
SOFTWARE
HOH G:522 , HOH G:1011 , HOH H:432 , HOH H:1213 , HOH I:438 , HOH I:714
BINDING SITE FOR RESIDUE NA H 431
22
DC7
SOFTWARE
HIS J:26 , HIS J:28 , HIS J:49 , TYR J:50 , ARG J:170 , MET J:258 , TRP J:325 , TRP J:326 , ASP J:355 , ARG J:357 , ZN J:430 , HOH J:507 , HOH J:530 , HOH J:1868
BINDING SITE FOR RESIDUE RAT J 428
23
DC8
SOFTWARE
ARG J:314 , LYS J:315 , HOH J:1844 , HIS L:49 , TYR L:50 , ALA L:53 , TRP L:326 , PHE L:327
BINDING SITE FOR RESIDUE CO3 J 429
24
DC9
SOFTWARE
HIS J:26 , HIS J:28 , ASP J:355 , RAT J:428
BINDING SITE FOR RESIDUE ZN J 430
25
EC1
SOFTWARE
LYS J:278 , GLU J:304 , LYS K:278 , GLU K:304 , LYS L:278 , GLU L:304
BINDING SITE FOR RESIDUE CL J 431
26
EC2
SOFTWARE
HIS K:26 , HIS K:28 , HIS K:49 , TYR K:50 , ARG K:170 , MET K:258 , TRP K:325 , TRP K:326 , ASP K:355 , ARG K:357 , ZN K:431 , HOH K:480 , HOH K:519 , HOH K:560 , HOH K:1872
BINDING SITE FOR RESIDUE RAT K 428
27
EC3
SOFTWARE
HIS J:49 , TYR J:50 , TRP J:326 , PHE J:327 , ARG K:314 , LYS K:315 , HOH K:1842
BINDING SITE FOR RESIDUE CO3 K 429
28
EC4
SOFTWARE
HIS K:49 , TYR K:50 , TRP K:326 , PHE K:327 , HOH K:1843 , ARG L:314 , LYS L:315
BINDING SITE FOR RESIDUE CO3 K 430
29
EC5
SOFTWARE
HIS K:26 , HIS K:28 , ASP K:355 , RAT K:428
BINDING SITE FOR RESIDUE ZN K 431
30
EC6
SOFTWARE
HIS L:26 , HIS L:28 , HIS L:49 , TYR L:50 , ARG L:170 , MET L:258 , TRP L:325 , TRP L:326 , ASP L:355 , ARG L:357 , ZN L:429 , HOH L:440 , HOH L:573 , HOH L:822
BINDING SITE FOR RESIDUE RAT L 428
31
EC7
SOFTWARE
HIS L:26 , HIS L:28 , ASP L:355 , RAT L:428
BINDING SITE FOR RESIDUE ZN L 429
32
EC8
SOFTWARE
HOH J:585 , HOH J:1661 , HOH K:462 , HOH K:1264 , HOH L:431 , HOH L:577
BINDING SITE FOR RESIDUE NA L 430
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
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PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
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End label:
Sorry, no Info available
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 12)
Info
All SCOP Domains
1a: SCOP_d3hk7a_ (A:)
1b: SCOP_d3hk7b_ (B:)
1c: SCOP_d3hk7c_ (C:)
1d: SCOP_d3hk7d_ (D:)
1e: SCOP_d3hk7e_ (E:)
1f: SCOP_d3hk7f_ (F:)
1g: SCOP_d3hk7g_ (G:)
1h: SCOP_d3hk7h_ (H:)
1i: SCOP_d3hk7i_ (I:)
1j: SCOP_d3hk7j_ (J:)
1k: SCOP_d3hk7k_ (K:)
1l: SCOP_d3hk7l_ (L:)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Metallo-dependent hydrolases
(273)
Family
:
Uronate isomerase-like
(10)
Protein domain
:
Uncharacterized protein BH0493
(9)
Bacillus halodurans [TaxId: 86665]
(9)
1a
d3hk7a_
A:
1b
d3hk7b_
B:
1c
d3hk7c_
C:
1d
d3hk7d_
D:
1e
d3hk7e_
E:
1f
d3hk7f_
F:
1g
d3hk7g_
G:
1h
d3hk7h_
H:
1i
d3hk7i_
I:
1j
d3hk7j_
J:
1k
d3hk7k_
K:
1l
d3hk7l_
L:
[
close SCOP info
]
CATH Domains
(1, 12)
Info
all CATH domains
1a: CATH_3hk7A02 (A:39-120)
1b: CATH_3hk7B02 (B:39-120)
1c: CATH_3hk7C02 (C:39-120)
1d: CATH_3hk7D02 (D:39-120)
1e: CATH_3hk7E02 (E:39-120)
1f: CATH_3hk7F02 (F:39-120)
1g: CATH_3hk7G02 (G:39-120)
1h: CATH_3hk7H02 (H:39-120)
1i: CATH_3hk7I02 (I:39-120)
1j: CATH_3hk7J02 (J:39-120)
1k: CATH_3hk7K02 (K:39-120)
1l: CATH_3hk7L02 (L:39-120)
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Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
uronate isomerase, domain 2, chain A
(11)
Homologous Superfamily
:
uronate isomerase, domain 2, chain A
(11)
Bacillus halodurans c-125. Organism_taxid: 272558. Strain: c-125 / dsm18197 / ferm 7344 / jcm 9153.
(5)
1a
3hk7A02
A:39-120
1b
3hk7B02
B:39-120
1c
3hk7C02
C:39-120
1d
3hk7D02
D:39-120
1e
3hk7E02
E:39-120
1f
3hk7F02
F:39-120
1g
3hk7G02
G:39-120
1h
3hk7H02
H:39-120
1i
3hk7I02
I:39-120
1j
3hk7J02
J:39-120
1k
3hk7K02
K:39-120
1l
3hk7L02
L:39-120
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Asymmetric Unit 1
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