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2GYI
Biol. Unit 1
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Asym.Unit (142 KB)
Biol.Unit 1 (266 KB)
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(1)
Title
:
DESIGN, SYNTHESIS, AND CHARACTERIZATION OF A POTENT XYLOSE ISOMERASE INHIBITOR, D-THREONOHYDROXAMIC ACID, AND HIGH-RESOLUTION X-RAY CRYSTALLOGRAPHIC STRUCTURE OF THE ENZYME-INHIBITOR COMPLEX
Authors
:
K. N. Allen, A. Lavie, G. A. Petsko, D. Ringe
Date
:
01 Sep 94 (Deposition) - 10 Jul 95 (Release) - 16 Nov 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.60
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (2x)
Keywords
:
Isomerase(Intramolecular Oxidoreductase)
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. N. Allen, A. Lavie, G. A. Petsko, D. Ringe
Design, Synthesis, And Characterization Of A Potent Xylose Isomerase Inhibitor, D-Threonohydroxamic Acid, And High-Resolution X-Ray Crystallographic Structure Of The Enzyme-Inhibitor Complex
Biochemistry V. 34 3742 1995
(for further references see the
PDB file header
)
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Hetero Components
(1, 4)
Info
All Hetero Components
1a: 2,3,4,N-TETRAHYDROXY-BUTYRIMIDIC A... (HYAa)
1b: 2,3,4,N-TETRAHYDROXY-BUTYRIMIDIC A... (HYAb)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
View:
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Label:
No.
Name
Count
Type
Full Name
1
HYA
4
Ligand/Ion
2,3,4,N-TETRAHYDROXY-BUTYRIMIDIC ACID
2
MG
-1
Ligand/Ion
MAGNESIUM ION
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Sites
(12, 12)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: HYA (AUTHOR)
08: HYB (AUTHOR)
09: M1A (AUTHOR)
10: M1B (AUTHOR)
11: M2A (AUTHOR)
12: M2B (AUTHOR)
View:
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:180 , GLU A:216 , ASP A:244 , ASP A:286 , HYA A:960
BINDING SITE FOR RESIDUE MG A 400
02
AC2
SOFTWARE
GLU A:216 , HIS A:219 , ASP A:256 , HYA A:960 , HOH A:1700 , HOH A:1701
BINDING SITE FOR RESIDUE MG A 401
03
AC3
SOFTWARE
GLU B:180 , GLU B:216 , ASP B:244 , ASP B:286 , MG B:401 , HYA B:970
BINDING SITE FOR RESIDUE MG B 400
04
AC4
SOFTWARE
GLU B:216 , HIS B:219 , MG B:400 , HYA B:970 , HOH B:1800 , HOH B:1801
BINDING SITE FOR RESIDUE MG B 401
05
AC5
SOFTWARE
TRP A:15 , HIS A:53 , PHE A:93 , TRP A:136 , GLU A:180 , LYS A:182 , GLU A:216 , HIS A:219 , ASP A:244 , ASP A:286 , MG A:400 , MG A:401 , HOH A:1166 , HOH A:1170 , HOH A:1338 , HOH A:1700 , PHE B:25
BINDING SITE FOR RESIDUE HYA A 960
06
AC6
SOFTWARE
PHE A:25 , TRP B:15 , HIS B:53 , PHE B:93 , TRP B:136 , GLU B:180 , LYS B:182 , HIS B:219 , ASP B:244 , ASP B:286 , MG B:400 , MG B:401 , HOH B:1279 , HOH B:1281 , HOH B:1539 , HOH B:1800
BINDING SITE FOR RESIDUE HYA B 970
07
HYA
AUTHOR
HYA A:960 , LYS A:182 , HIS A:53
INHIBITOR, D-THREONOHYDROXAMIC ACID BINDING SITE IN MONOMER A
08
HYB
AUTHOR
HYA B:970 , LYS B:182 , HIS B:53
INHIBITOR, D-THREONOHYDROXAMIC ACID BINDING SITE IN MONOMER B
09
M1A
AUTHOR
MG A:400 , GLU A:180 , ASP A:244 , ASP A:286 , GLU A:216 , HYA A:960
METAL BINDING SITE 1 IN MONOMER A ACTIVE SITE
10
M1B
AUTHOR
MG B:400 , GLU B:180 , ASP B:244 , ASP B:286 , GLU B:216 , HYA B:970
METAL BINDING SITE 1 IN MONOMER B ACTIVE SITE
11
M2A
AUTHOR
MG A:401 , GLU A:216 , HIS A:219 , HYA A:960 , HOH A:1700 , HOH A:1701
METAL BINDING SITE 2 IN MONOMER A ACTIVE SITE
12
M2B
AUTHOR
MG B:401 , GLU B:216 , HIS B:219 , HYA B:970 , HOH B:1800 , HOH B:1801
METAL BINDING SITE 2 IN MONOMER B ACTIVE SITE
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: XYLOSE_ISOMERASE (A:3-382,B:3-382)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
XYLOSE_ISOMERASE
PS51415
Xylose isomerase family profile.
XYLA_STROL
4-383
4
A:3-382
B:3-382
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Exons
(0, 0)
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d2gyia_ (A:)
1b: SCOP_d2gyib_ (B:)
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)
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)
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)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Xylose isomerase-like
(125)
Family
:
Xylose isomerase
(97)
Protein domain
:
D-xylose isomerase
(82)
Streptomyces olivochromogenes [TaxId: 1963]
(9)
1a
d2gyia_
A:
1b
d2gyib_
B:
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_2gyiA00 (A:2-386)
1b: CATH_2gyiB00 (B:2-386)
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Organisms
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Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Divalent-metal-dependent TIM barrel enzymes
(98)
Streptomyces olivochromogenes. Organism_taxid: 1963
(6)
1a
2gyiA00
A:2-386
1b
2gyiB00
B:2-386
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Pfam Domains
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Asym.Unit (142 KB)
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