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3HK9
Asym. Unit
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
[
close entry info
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Hetero Components
(4, 40)
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
4
Ligand/Ion
CHLORIDE ION
2
CO3
12
Ligand/Ion
CARBONATE ION
3
REL
12
Ligand/Ion
D-GLUCURONIC ACID
4
ZN
12
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(40, 40)
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)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:26 , HIS A:28 , HIS A:49 , TYR A:50 , ARG A:170 , MET A:258 , TRP A:325 , TRP A:326 , ASP A:355 , ARG A:357 , ZN A:431 , HOH A:922 , HOH A:1409 , HOH A:1908
BINDING SITE FOR RESIDUE REL A 428
02
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
03
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
04
AC4
SOFTWARE
HIS A:26 , HIS A:28 , ASP A:355 , REL A:428
BINDING SITE FOR RESIDUE ZN A 431
05
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
06
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
07
AC7
SOFTWARE
HIS B:26 , HIS B:28 , ASP B:355 , REL B:428
BINDING SITE FOR RESIDUE ZN B 429
08
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
09
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
10
BC1
SOFTWARE
HIS C:26 , HIS C:28 , ASP C:355 , REL C:428
BINDING SITE FOR RESIDUE ZN C 430
11
BC2
SOFTWARE
HIS D:26 , HIS D:28 , HIS D:49 , TYR D:50 , ARG D:170 , SER D:223 , MET D:258 , TRP D:325 , TRP D:326 , ASP D:355 , ARG D:357 , ZN D:431 , HOH D:438 , HOH D:484 , HOH D:1045
BINDING SITE FOR RESIDUE REL D 428
12
BC3
SOFTWARE
HIS D:49 , TYR D:50 , TRP D:326 , PHE D:327 , HOH D:1046 , ARG E:314 , LYS E:315
BINDING SITE FOR RESIDUE CO3 D 429
13
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
14
BC5
SOFTWARE
HIS D:26 , HIS D:28 , ASP D:355 , REL D:428
BINDING SITE FOR RESIDUE ZN D 431
15
BC6
SOFTWARE
HIS E:26 , HIS E:28 , HIS E:49 , TYR E:50 , ARG E:170 , SER E:223 , MET E:258 , TRP E:325 , TRP E:326 , ASP E:355 , ARG E:357 , ZN E:429 , HOH E:716 , HOH E:1263
BINDING SITE FOR RESIDUE REL E 428
16
BC7
SOFTWARE
HIS E:26 , HIS E:28 , ASP E:355 , REL E:428
BINDING SITE FOR RESIDUE ZN E 429
17
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
18
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
19
CC1
SOFTWARE
HIS F:26 , HIS F:28 , ASP F:355 , REL F:428
BINDING SITE FOR RESIDUE ZN F 430
20
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
21
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
22
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
23
CC5
SOFTWARE
HIS G:26 , HIS G:28 , ASP G:355 , REL G:428
BINDING SITE FOR RESIDUE ZN G 430
24
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
25
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
26
CC8
SOFTWARE
HIS H:26 , HIS H:28 , ASP H:355 , REL H:428
BINDING SITE FOR RESIDUE ZN H 430
27
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
28
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
29
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
30
DC3
SOFTWARE
HIS I:26 , HIS I:28 , ASP I:355 , REL I:428
BINDING SITE FOR RESIDUE ZN I 430
31
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
32
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
33
DC6
SOFTWARE
HIS J:26 , HIS J:28 , ASP J:355 , REL J:428
BINDING SITE FOR RESIDUE ZN J 430
34
DC7
SOFTWARE
HIS K:26 , HIS K:28 , HIS K:49 , TYR K:50 , ARG K:170 , SER K:223 , MET K:258 , LYS K:263 , TRP K:325 , TRP K:326 , ASP K:355 , ARG K:357 , ZN K:430 , HOH K:436 , HOH K:605 , HOH K:1456
BINDING SITE FOR RESIDUE REL K 428
35
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
36
DC9
SOFTWARE
HIS K:26 , HIS K:28 , ASP K:355 , REL K:428
BINDING SITE FOR RESIDUE ZN K 430
37
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
38
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
39
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
40
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 not available)
All SNPs/Variants
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
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End label:
Sorry, no Info available
[
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Exons
(0, 0)
Info
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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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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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)
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
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