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3HK9
Biol. Unit 3
Info
Asym.Unit (866 KB)
Biol.Unit 1 (505 KB)
Biol.Unit 2 (505 KB)
Biol.Unit 3 (575 KB)
Biol.Unit 4 (505 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF URONATE ISOMERASE FROM BACILLUS HALODURANS COMPLEXED WITH ZINC AND D-GLUCURONATE
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) - 16 Oct 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,C,D,E,H,K (1x)
Biol. Unit 2: A,B,D,E,F,I,L (1x)
Biol. Unit 3: B,C,F,G,H,I,J,L (1x)
Biol. Unit 4: C,D,G,H,J,K,L (1x)
Keywords
:
Uronate Isomerase, D-Glucuronate, Mechanism Of The Reaction, Isomerase
(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 Isomeras Illustrates How An Isomerase May Have Evolved From A Hydrolase Within The Amidohydrolase Superfamily.
Biochemistry V. 48 8879 2009
[
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Hetero Components
(2, 15)
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: D-GLUCURONIC ACID (RELa)
3b: D-GLUCURONIC ACID (RELb)
3c: D-GLUCURONIC ACID (RELc)
3d: D-GLUCURONIC ACID (RELd)
3e: D-GLUCURONIC ACID (RELe)
3f: D-GLUCURONIC ACID (RELf)
3g: D-GLUCURONIC ACID (RELg)
3h: D-GLUCURONIC ACID (RELh)
3i: D-GLUCURONIC ACID (RELi)
3j: D-GLUCURONIC ACID (RELj)
3k: D-GLUCURONIC ACID (RELk)
3l: D-GLUCURONIC ACID (RELl)
4a: ZINC ION (ZNa)
4b: ZINC ION (ZNb)
4c: ZINC ION (ZNc)
4d: ZINC ION (ZNd)
4e: ZINC ION (ZNe)
4f: ZINC ION (ZNf)
4g: ZINC ION (ZNg)
4h: ZINC ION (ZNh)
4i: ZINC ION (ZNi)
4j: ZINC ION (ZNj)
4k: ZINC ION (ZNk)
4l: ZINC ION (ZNl)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
-1
Ligand/Ion
CHLORIDE ION
2
CO3
7
Ligand/Ion
CARBONATE ION
3
REL
8
Ligand/Ion
D-GLUCURONIC ACID
4
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(31, 31)
Info
All Sites
01: AC2 (SOFTWARE)
02: AC3 (SOFTWARE)
03: AC5 (SOFTWARE)
04: AC6 (SOFTWARE)
05: AC7 (SOFTWARE)
06: AC8 (SOFTWARE)
07: AC9 (SOFTWARE)
08: BC1 (SOFTWARE)
09: BC4 (SOFTWARE)
10: BC8 (SOFTWARE)
11: BC9 (SOFTWARE)
12: CC1 (SOFTWARE)
13: CC2 (SOFTWARE)
14: CC3 (SOFTWARE)
15: CC4 (SOFTWARE)
16: CC5 (SOFTWARE)
17: CC6 (SOFTWARE)
18: CC7 (SOFTWARE)
19: CC8 (SOFTWARE)
20: CC9 (SOFTWARE)
21: DC1 (SOFTWARE)
22: DC2 (SOFTWARE)
23: DC3 (SOFTWARE)
24: DC4 (SOFTWARE)
25: DC5 (SOFTWARE)
26: DC6 (SOFTWARE)
27: DC8 (SOFTWARE)
28: EC1 (SOFTWARE)
29: EC2 (SOFTWARE)
30: EC3 (SOFTWARE)
31: EC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC2
SOFTWARE
HIS A:49 , TYR A:50 , TRP A:326 , PHE A:327 , HOH A:936 , ARG B:314 , LYS B:315
BINDING SITE FOR RESIDUE CO3 A 429
02
AC3
SOFTWARE
ARG A:314 , LYS A:315 , HIS C:49 , TYR C:50 , ALA C:53 , TRP C:326 , PHE C:327 , HOH C:452
BINDING SITE FOR RESIDUE CO3 A 430
03
AC5
SOFTWARE
LYS A:278 , GLU A:304 , LYS B:278 , GLU B:304 , LYS C:278 , GLU C:304
BINDING SITE FOR RESIDUE CL A 432
04
AC6
SOFTWARE
HIS B:26 , HIS B:28 , HIS B:49 , TYR B:50 , ARG B:170 , SER B:223 , MET B:258 , TRP B:325 , TRP B:326 , ASP B:355 , ARG B:357 , ZN B:429 , HOH B:432 , HOH B:449
BINDING SITE FOR RESIDUE REL B 428
05
AC7
SOFTWARE
HIS B:26 , HIS B:28 , ASP B:355 , REL B:428
BINDING SITE FOR RESIDUE ZN B 429
06
AC8
SOFTWARE
HIS C:26 , HIS C:28 , HIS C:49 , TYR C:50 , ARG C:170 , SER C:223 , MET C:258 , TRP C:325 , TRP C:326 , ASP C:355 , ARG C:357 , ZN C:430 , HOH C:459 , HOH C:1171 , HOH C:1690
BINDING SITE FOR RESIDUE REL C 428
07
AC9
SOFTWARE
HIS B:49 , TYR B:50 , TRP B:326 , PHE B:327 , HOH B:822 , ARG C:314 , LYS C:315
BINDING SITE FOR RESIDUE CO3 C 429
08
BC1
SOFTWARE
HIS C:26 , HIS C:28 , ASP C:355 , REL C:428
BINDING SITE FOR RESIDUE ZN C 430
09
BC4
SOFTWARE
ARG D:314 , LYS D:315 , HIS F:49 , TYR F:50 , TRP F:326 , PHE F:327 , HOH F:443
BINDING SITE FOR RESIDUE CO3 D 430
10
BC8
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:430 , HOH F:470 , HOH F:1133 , HOH F:1155
BINDING SITE FOR RESIDUE REL F 428
11
BC9
SOFTWARE
HIS E:49 , TYR E:50 , ALA E:53 , TRP E:326 , PHE E:327 , HOH E:435 , ARG F:314 , LYS F:315
BINDING SITE FOR RESIDUE CO3 F 429
12
CC1
SOFTWARE
HIS F:26 , HIS F:28 , ASP F:355 , REL F:428
BINDING SITE FOR RESIDUE ZN F 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 F 431
14
CC3
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:649 , HOH G:1382
BINDING SITE FOR RESIDUE REL G 428
15
CC4
SOFTWARE
ARG G:314 , LYS G:315 , HIS I:49 , TYR I:50 , TRP I:326 , PHE I:327 , HOH I:448
BINDING SITE FOR RESIDUE CO3 G 429
16
CC5
SOFTWARE
HIS G:26 , HIS G:28 , ASP G:355 , REL G:428
BINDING SITE FOR RESIDUE ZN G 430
17
CC6
SOFTWARE
HIS H:26 , HIS H:28 , HIS H:49 , TYR H:50 , ARG H:170 , SER H:223 , MET H:258 , TRP H:325 , TRP H:326 , ASP H:355 , ARG H:357 , ZN H:430 , HOH H:452 , HOH H:464 , HOH H:1537
BINDING SITE FOR RESIDUE REL H 428
18
CC7
SOFTWARE
HIS G:49 , TYR G:50 , ALA G:53 , TRP G:326 , PHE G:327 , ARG H:314 , LYS H:315 , HOH H:799
BINDING SITE FOR RESIDUE CO3 H 429
19
CC8
SOFTWARE
HIS H:26 , HIS H:28 , ASP H:355 , REL H:428
BINDING SITE FOR RESIDUE ZN H 430
20
CC9
SOFTWARE
LYS G:278 , GLU G:304 , LYS H:278 , GLU H:304 , LYS I:278 , GLU I:304
BINDING SITE FOR RESIDUE CL H 431
21
DC1
SOFTWARE
HIS I:26 , HIS I:28 , HIS I:49 , TYR I:50 , ARG I:170 , SER I:223 , MET I:258 , TRP I:325 , TRP I:326 , ASP I:355 , ARG I:357 , ZN I:430 , HOH I:693 , HOH I:1212 , HOH I:1789
BINDING SITE FOR RESIDUE REL I 428
22
DC2
SOFTWARE
HIS H:49 , TYR H:50 , ALA H:53 , TRP H:326 , PHE H:327 , HOH H:495 , ARG I:314 , LYS I:315
BINDING SITE FOR RESIDUE CO3 I 429
23
DC3
SOFTWARE
HIS I:26 , HIS I:28 , ASP I:355 , REL I:428
BINDING SITE FOR RESIDUE ZN I 430
24
DC4
SOFTWARE
HIS J:26 , HIS J:28 , HIS J:49 , TYR J:50 , ARG J:170 , SER J:223 , MET J:258 , TRP J:325 , TRP J:326 , ASP J:355 , ARG J:357 , ZN J:430 , HOH J:956 , HOH J:1102 , HOH J:1336
BINDING SITE FOR RESIDUE REL J 428
25
DC5
SOFTWARE
ARG J:314 , LYS J:315 , HIS L:49 , TYR L:50 , TRP L:326 , PHE L:327 , HOH L:438
BINDING SITE FOR RESIDUE CO3 J 429
26
DC6
SOFTWARE
HIS J:26 , HIS J:28 , ASP J:355 , REL J:428
BINDING SITE FOR RESIDUE ZN J 430
27
DC8
SOFTWARE
HIS J:49 , TYR J:50 , TRP J:326 , PHE J:327 , HOH J:864 , ARG K:314 , LYS K:315
BINDING SITE FOR RESIDUE CO3 K 429
28
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 K 431
29
EC2
SOFTWARE
HIS L:26 , HIS L:28 , HIS L:49 , TYR L:50 , ARG L:170 , SER L:223 , MET L:258 , TRP L:325 , TRP L:326 , ASP L:355 , ARG L:357 , ZN L:430 , HOH L:481 , HOH L:934 , HOH L:1210
BINDING SITE FOR RESIDUE REL L 428
30
EC3
SOFTWARE
HIS K:49 , TYR K:50 , ALA K:272 , TRP K:326 , PHE K:327 , HOH K:547 , ARG L:314 , LYS L:315
BINDING SITE FOR RESIDUE CO3 L 429
31
EC4
SOFTWARE
HIS L:26 , HIS L:28 , ASP L:355 , REL L:428
BINDING SITE FOR RESIDUE ZN L 430
[
close Site info
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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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[
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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_d3hk9a_ (A:)
1b: SCOP_d3hk9b_ (B:)
1c: SCOP_d3hk9c_ (C:)
1d: SCOP_d3hk9d_ (D:)
1e: SCOP_d3hk9e_ (E:)
1f: SCOP_d3hk9f_ (F:)
1g: SCOP_d3hk9g_ (G:)
1h: SCOP_d3hk9h_ (H:)
1i: SCOP_d3hk9i_ (I:)
1j: SCOP_d3hk9j_ (J:)
1k: SCOP_d3hk9k_ (K:)
1l: SCOP_d3hk9l_ (L:)
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)
(
)
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
d3hk9a_
A:
1b
d3hk9b_
B:
1c
d3hk9c_
C:
1d
d3hk9d_
D:
1e
d3hk9e_
E:
1f
d3hk9f_
F:
1g
d3hk9g_
G:
1h
d3hk9h_
H:
1i
d3hk9i_
I:
1j
d3hk9j_
J:
1k
d3hk9k_
K:
1l
d3hk9l_
L:
[
close SCOP info
]
CATH Domains
(1, 12)
Info
all CATH domains
1a: CATH_3hk9A02 (A:39-120)
1b: CATH_3hk9H02 (H:39-120)
1c: CATH_3hk9I02 (I:39-120)
1d: CATH_3hk9J02 (J:39-120)
1e: CATH_3hk9K02 (K:39-120)
1f: CATH_3hk9L02 (L:39-120)
1g: CATH_3hk9B02 (B:39-120)
1h: CATH_3hk9C02 (C:39-120)
1i: CATH_3hk9D02 (D:39-120)
1j: CATH_3hk9E02 (E:39-120)
1k: CATH_3hk9F02 (F:39-120)
1l: CATH_3hk9G02 (G:39-120)
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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
3hk9A02
A:39-120
1b
3hk9H02
H:39-120
1c
3hk9I02
I:39-120
1d
3hk9J02
J:39-120
1e
3hk9K02
K:39-120
1f
3hk9L02
L:39-120
1g
3hk9B02
B:39-120
1h
3hk9C02
C:39-120
1i
3hk9D02
D:39-120
1j
3hk9E02
E:39-120
1k
3hk9F02
F:39-120
1l
3hk9G02
G:39-120
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Chain L
Asymmetric Unit 1
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Asym.Unit (866 KB)
Header - Asym.Unit
Biol.Unit 1 (505 KB)
Header - Biol.Unit 1
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Biol.Unit 3 (575 KB)
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