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1YXD
Asym. Unit
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Asym.Unit (104 KB)
Biol.Unit 1 (195 KB)
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(1)
Title
:
STRUCTURE OF E. COLI DIHYDRODIPICOLINATE SYNTHASE BOUND WITH ALLOSTERIC INHIBITOR (S)-LYSINE TO 2.0 A
Authors
:
R. C. J. Dobson, M. D. W. Griffin, G. B. Jameson, J. A. Gerrard
Date
:
20 Feb 05 (Deposition) - 02 Aug 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (2x)
Keywords
:
Dihydrodipicolinate Synthase, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. C. Dobson, M. D. Griffin, G. B. Jameson, J. A. Gerrard
The Crystal Structures Of Native And (S)-Lysine-Bound Dihydrodipicolinate Synthase From Escherichia Coli With Improved Resolution Show New Features Of Biological Significance.
Acta Crystallogr. , Sect. D V. 61 1116 2005
(for further references see the
PDB file header
)
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Hetero Components
(3, 7)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
2a: POTASSIUM ION (Ka)
2b: POTASSIUM ION (Kb)
3a: LYSINE (LYSa)
3b: LYSINE (LYSb)
3c: LYSINE (LYSc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
2
Ligand/Ion
CHLORIDE ION
2
K
2
Ligand/Ion
POTASSIUM ION
3
LYS
3
Mod. Amino Acid
LYSINE
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Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ALA A:152 , VAL A:154 , LYS A:155 , ILE A:157
BINDING SITE FOR RESIDUE K A 1301
2
AC2
SOFTWARE
GLY A:43 , THR A:44 , LEU A:101 , LYS A:161 , HOH A:1345 , HOH A:1349
BINDING SITE FOR RESIDUE CL A 1302
3
AC3
SOFTWARE
ALA B:152 , VAL B:154 , LYS B:155 , ILE B:157 , HOH B:3498 , HOH B:3584
BINDING SITE FOR RESIDUE K B 2301
4
AC4
SOFTWARE
THR B:44 , LEU B:101 , LYS B:161 , HOH B:3342 , HOH B:3360
BINDING SITE FOR RESIDUE CL B 2302
5
AC5
SOFTWARE
SER A:48 , ALA A:49 , LEU A:51 , HIS A:53 , HIS A:56 , TYR A:106 , HOH A:1436 , ASN B:80 , GLU B:84 , LYS B:2300 , HOH B:3302 , HOH B:3304
BINDING SITE FOR RESIDUE LYS B 1300
6
AC6
SOFTWARE
ASN A:80 , GLU A:84 , SER B:48 , ALA B:49 , LEU B:51 , HIS B:56 , TYR B:106 , LYS B:1300 , HOH B:3375 , HOH B:3432
BINDING SITE FOR RESIDUE LYS B 2300
7
AC7
SOFTWARE
HOH A:1482 , ALA B:33 , HOH B:3305 , HOH B:3308
BINDING SITE FOR RESIDUE LYS B 3301
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: DHDPS_1 (A:38-55,B:38-55)
2: DHDPS_2 (A:133-163,B:133-163)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
DHDPS_1
PS00665
Dihydrodipicolinate synthase signature 1.
DAPA_ECOLI
38-55
2
A:38-55
B:38-55
2
DHDPS_2
PS00666
Dihydrodipicolinate synthase signature 2.
DAPA_ECOLI
133-163
2
A:133-163
B:133-163
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Exons
(0, 0)
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All Exons
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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, 2)
Info
All SCOP Domains
1a: SCOP_d1yxda_ (A:)
1b: SCOP_d1yxdb_ (B:)
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)
Protein Domains
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(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Aldolase
(457)
Family
:
Class I aldolase
(182)
Protein domain
:
Dihydrodipicolinate synthase
(30)
Escherichia coli [TaxId: 562]
(15)
1a
d1yxda_
A:
1b
d1yxdb_
B:
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1yxdA00 (A:1-292)
1b: CATH_1yxdB00 (B:1-292)
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Organisms
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Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Aldolase class I
(887)
Escherichia coli. Organism_taxid: 562.
(43)
1a
1yxdA00
A:1-292
1b
1yxdB00
B:1-292
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Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_DHDPS_1yxdB01 (B:1-290)
1b: PFAM_DHDPS_1yxdB02 (B:1-290)
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Clan
:
TIM_barrel
(694)
Family
:
DHDPS
(40)
Escherichia coli (strain K12)
(27)
1a
DHDPS-1yxdB01
B:1-290
1b
DHDPS-1yxdB02
B:1-290
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Asymmetric Unit 1
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Asym.Unit (104 KB)
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