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2GKE
Asym. Unit
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Asym.Unit (107 KB)
Biol.Unit 1 (103 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF DIAMINOPIMELATE EPIMERASE IN COMPLEX WITH AN IRREVERSIBLE INHIBITOR LL-AZIDAP
Authors
:
B. Pillai, M. M. Cherney, C. M. Diaper, A. Sutherland, J. S. Blanchard, J. C. Vederas, M. N. James
Date
:
01 Apr 06 (Deposition) - 16 May 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.35
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Enzyme-Inhibitor Complex, Covalently Bound Inhibitor, Isomerase
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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Reference
:
B. Pillai, M. M. Cherney, C. M. Diaper, A. Sutherland, J. S. Blanchard, J. C. Vederas, M. N. James
Structural Insights Into Stereochemical Inversion By Diaminopimelate Epimerase: An Antibacterial Drug Target.
Proc. Natl. Acad. Sci. Usa V. 103 8668 2006
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Hetero Components
(3, 5)
Info
All Hetero Components
1a: ACETIC ACID (ACYa)
1b: ACETIC ACID (ACYb)
1c: ACETIC ACID (ACYc)
2a: GLYCEROL (GOLa)
3a: (2S,6S)-2,6-DIAMINO-2-METHYLHEPTAN... (ZDPa)
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No.
Name
Count
Type
Full Name
1
ACY
3
Ligand/Ion
ACETIC ACID
2
GOL
1
Ligand/Ion
GLYCEROL
3
ZDP
1
Ligand/Ion
(2S,6S)-2,6-DIAMINO-2-METHYLHEPTANEDIOIC ACID
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Sites
(5, 5)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASN A:11 , GLN A:44 , ASN A:64 , VAL A:70 , GLN A:72 , CYS A:73 , GLY A:74 , ASN A:75 , ASN A:157 , ASN A:190 , GLU A:208 , ARG A:209 , CYS A:217 , GLY A:218 , SER A:219
BINDING SITE FOR RESIDUE ZDP A 700
2
AC2
SOFTWARE
THR A:26 , THR A:29 , GLU A:124 , ASN A:133 , LYS A:134 , PHE A:135 , LEU A:274 , HOH A:310 , HOH A:497 , HOH A:591
BINDING SITE FOR RESIDUE GOL A 694
3
AC3
SOFTWARE
TYR A:139 , ILE A:140 , ARG A:184 , HOH A:340 , HOH A:373 , HOH A:493
BINDING SITE FOR RESIDUE ACY A 695
4
AC4
SOFTWARE
GLU A:69 , SER A:71 , GLN A:100 , LYS A:101 , HIS A:256 , HOH A:319 , HOH A:492
BINDING SITE FOR RESIDUE ACY A 696
5
AC5
SOFTWARE
GLU A:187 , ARG A:188 , GLY A:255 , HOH A:674
BINDING SITE FOR RESIDUE ACY A 697
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are not available)
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: DAP_EPIMERASE (A:64-78)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
DAP_EPIMERASE
PS01326
Diaminopimelate epimerase signature.
DAPF_HAEIN
64-78
1
A:64-78
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Exons
(0, 0)
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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_d2gkea1 (A:1-130)
1b: SCOP_d2gkea2 (A:131-274)
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)
Protein Domains
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)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Diaminopimelate epimerase-like
(37)
Superfamily
:
Diaminopimelate epimerase-like
(37)
Family
:
Diaminopimelate epimerase
(8)
Protein domain
:
Diaminopimelate epimerase
(8)
Haemophilus influenzae [TaxId: 727]
(6)
1a
d2gkea1
A:1-130
1b
d2gkea2
A:131-274
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_2gkeA02 (A:115-139,A:150-261)
1b: CATH_2gkeA01 (A:1-114,A:262-274)
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Organisms
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Class
:
Alpha Beta
(26913)
Architecture
:
Roll
(3276)
Topology
:
Diaminopimelate Epimerase; Chain A, domain 1
(22)
Homologous Superfamily
:
Diaminopimelate Epimerase; Chain A, domain 1
(22)
Haemophilus influenzae. Organism_taxid: 727.
(5)
1a
2gkeA02
A:115-139,A:150-261
1b
2gkeA01
A:1-114,A:262-274
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Pfam Domains
(0, 0)
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Chain A
Asymmetric Unit 1
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Asym.Unit (107 KB)
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