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Asym. Unit
Info
Asym.Unit (866 KB)
Biol.Unit 1 (433 KB)
Biol.Unit 2 (435 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF APO DIPEPTIDE EPIMERASE FROM THERMOTOGA MARITIMA
Authors
:
A. A. Fedorov, E. V. Fedorov, H. J. Imker, J. A. Gerlt, S. C. Almo
Date
:
12 Jun 08 (Deposition) - 25 Nov 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Biol. Unit 1: A,B,C,D,E,F,G,H (1x)
Biol. Unit 2: I,J,K,L,M,N,O,P (1x)
Keywords
:
Dipeptide Epimerase, Thermotoga Maritima, Enzymatic Function, Isomerase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. Kalyanaraman, H. J. Imker, A. A. Fedorov, E. V. Fedorov, M. E. Glasner, P. C. Babbitt, S. C. Almo, J. A. Gerlt, M. P. Jacobson
Discovery Of A Dipeptide Epimerase Enzymatic Function Guided By Homology Modeling And Virtual Screening.
Structure V. 16 1668 2008
(for further references see the
PDB file header
)
[
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Hetero Components
(1, 16)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
1c: MAGNESIUM ION (MGc)
1d: MAGNESIUM ION (MGd)
1e: MAGNESIUM ION (MGe)
1f: MAGNESIUM ION (MGf)
1g: MAGNESIUM ION (MGg)
1h: MAGNESIUM ION (MGh)
1i: MAGNESIUM ION (MGi)
1j: MAGNESIUM ION (MGj)
1k: MAGNESIUM ION (MGk)
1l: MAGNESIUM ION (MGl)
1m: MAGNESIUM ION (MGm)
1n: MAGNESIUM ION (MGn)
1o: MAGNESIUM ION (MGo)
1p: MAGNESIUM ION (MGp)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MG
16
Ligand/Ion
MAGNESIUM ION
[
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Sites
(16, 16)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:188 , GLU A:216 , ASP A:241
BINDING SITE FOR RESIDUE MG A 401
02
AC2
SOFTWARE
ASP B:188 , GLU B:216 , ASP B:241
BINDING SITE FOR RESIDUE MG B 401
03
AC3
SOFTWARE
ASP C:188 , GLU C:216 , ASP C:241
BINDING SITE FOR RESIDUE MG C 401
04
AC4
SOFTWARE
ASP D:188 , GLU D:216 , ASP D:241
BINDING SITE FOR RESIDUE MG D 401
05
AC5
SOFTWARE
ASP E:188 , GLU E:216 , ASP E:241
BINDING SITE FOR RESIDUE MG E 401
06
AC6
SOFTWARE
ASP F:188 , GLU F:216 , ASP F:241
BINDING SITE FOR RESIDUE MG F 401
07
AC7
SOFTWARE
ASP G:188 , GLU G:216 , ASP G:241
BINDING SITE FOR RESIDUE MG G 401
08
AC8
SOFTWARE
ASP H:188 , GLU H:216 , ASP H:241
BINDING SITE FOR RESIDUE MG H 401
09
AC9
SOFTWARE
ASP I:188 , GLU I:216 , ASP I:241
BINDING SITE FOR RESIDUE MG I 401
10
BC1
SOFTWARE
ASP J:188 , GLU J:216 , ASP J:241
BINDING SITE FOR RESIDUE MG J 401
11
BC2
SOFTWARE
ASP K:188 , GLU K:216 , ASP K:241
BINDING SITE FOR RESIDUE MG K 401
12
BC3
SOFTWARE
ASP L:188 , GLU L:216 , ASP L:241
BINDING SITE FOR RESIDUE MG L 401
13
BC4
SOFTWARE
ASP M:188 , GLU M:216 , ASP M:241 , GLU M:242
BINDING SITE FOR RESIDUE MG M 401
14
BC5
SOFTWARE
ASP N:188 , ASN N:190 , GLU N:216 , ASP N:241
BINDING SITE FOR RESIDUE MG N 401
15
BC6
SOFTWARE
ASP O:188 , GLU O:216 , ASP O:241
BINDING SITE FOR RESIDUE MG O 401
16
BC7
SOFTWARE
ASP P:188 , GLU P:216 , ASP P:241
BINDING SITE FOR RESIDUE MG P 401
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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End label:
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 32)
Info
All SCOP Domains
1a: SCOP_d3dfya1 (A:3-124)
1b: SCOP_d3dfyb1 (B:3-124)
1c: SCOP_d3dfyc1 (C:3-124)
1d: SCOP_d3dfyd1 (D:3-124)
1e: SCOP_d3dfye1 (E:3-124)
1f: SCOP_d3dfyf1 (F:3-124)
1g: SCOP_d3dfyg1 (G:3-124)
1h: SCOP_d3dfyh1 (H:3-124)
1i: SCOP_d3dfyi1 (I:3-124)
1j: SCOP_d3dfyj1 (J:3-124)
1k: SCOP_d3dfyk1 (K:3-124)
1l: SCOP_d3dfyl1 (L:3-124)
1m: SCOP_d3dfym1 (M:3-124)
1n: SCOP_d3dfyn1 (N:3-124)
1o: SCOP_d3dfyo1 (O:3-124)
1p: SCOP_d3dfyp1 (P:3-124)
2a: SCOP_d3dfya2 (A:125-343)
2b: SCOP_d3dfyb2 (B:125-343)
2c: SCOP_d3dfyc2 (C:125-343)
2d: SCOP_d3dfyd2 (D:125-343)
2e: SCOP_d3dfye2 (E:125-343)
2f: SCOP_d3dfyf2 (F:125-343)
2g: SCOP_d3dfyg2 (G:125-343)
2h: SCOP_d3dfyh2 (H:125-343)
2i: SCOP_d3dfyi2 (I:125-343)
2j: SCOP_d3dfyj2 (J:125-343)
2k: SCOP_d3dfyk2 (K:125-343)
2l: SCOP_d3dfyl2 (L:125-343)
2m: SCOP_d3dfym2 (M:125-343)
2n: SCOP_d3dfyn2 (N:125-343)
2o: SCOP_d3dfyo2 (O:125-343)
2p: SCOP_d3dfyp2 (P:125-343)
View:
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Classes
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)
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)
Folds
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)
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)
Superfamilies
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)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Enolase N-terminal domain-like
(211)
Superfamily
:
Enolase N-terminal domain-like
(211)
Family
:
automated matches
(123)
Protein domain
:
automated matches
(123)
Thermotoga maritima [TaxId: 243274]
(5)
1a
d3dfya1
A:3-124
1b
d3dfyb1
B:3-124
1c
d3dfyc1
C:3-124
1d
d3dfyd1
D:3-124
1e
d3dfye1
E:3-124
1f
d3dfyf1
F:3-124
1g
d3dfyg1
G:3-124
1h
d3dfyh1
H:3-124
1i
d3dfyi1
I:3-124
1j
d3dfyj1
J:3-124
1k
d3dfyk1
K:3-124
1l
d3dfyl1
L:3-124
1m
d3dfym1
M:3-124
1n
d3dfyn1
N:3-124
1o
d3dfyo1
O:3-124
1p
d3dfyp1
P:3-124
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Enolase C-terminal domain-like
(212)
Family
:
automated matches
(102)
Protein domain
:
automated matches
(102)
Thermotoga maritima [TaxId: 243274]
(5)
2a
d3dfya2
A:125-343
2b
d3dfyb2
B:125-343
2c
d3dfyc2
C:125-343
2d
d3dfyd2
D:125-343
2e
d3dfye2
E:125-343
2f
d3dfyf2
F:125-343
2g
d3dfyg2
G:125-343
2h
d3dfyh2
H:125-343
2i
d3dfyi2
I:125-343
2j
d3dfyj2
J:125-343
2k
d3dfyk2
K:125-343
2l
d3dfyl2
L:125-343
2m
d3dfym2
M:125-343
2n
d3dfyn2
N:125-343
2o
d3dfyo2
O:125-343
2p
d3dfyp2
P:125-343
[
close SCOP info
]
CATH Domains
(2, 32)
Info
all CATH domains
1a: CATH_3dfyA01 (A:3-115)
1b: CATH_3dfyI01 (I:3-115)
1c: CATH_3dfyM01 (M:3-115)
1d: CATH_3dfyF01 (F:3-115)
1e: CATH_3dfyB01 (B:3-115)
1f: CATH_3dfyD01 (D:3-115)
1g: CATH_3dfyN01 (N:3-115)
1h: CATH_3dfyP01 (P:3-115)
1i: CATH_3dfyH01 (H:3-115)
1j: CATH_3dfyJ01 (J:3-115)
1k: CATH_3dfyL01 (L:3-115)
1l: CATH_3dfyO01 (O:3-115)
1m: CATH_3dfyE01 (E:3-115)
1n: CATH_3dfyG01 (G:3-115)
1o: CATH_3dfyK01 (K:3-115)
1p: CATH_3dfyC01 (C:3-115)
2a: CATH_3dfyB02 (B:116-343)
2b: CATH_3dfyE02 (E:116-343)
2c: CATH_3dfyF02 (F:116-343)
2d: CATH_3dfyG02 (G:116-343)
2e: CATH_3dfyH02 (H:116-343)
2f: CATH_3dfyJ02 (J:116-343)
2g: CATH_3dfyK02 (K:116-343)
2h: CATH_3dfyL02 (L:116-343)
2i: CATH_3dfyN02 (N:116-343)
2j: CATH_3dfyO02 (O:116-343)
2k: CATH_3dfyP02 (P:116-343)
2l: CATH_3dfyA02 (A:116-343)
2m: CATH_3dfyC02 (C:116-343)
2n: CATH_3dfyI02 (I:116-343)
2o: CATH_3dfyM02 (M:116-343)
2p: CATH_3dfyD02 (D:116-343)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Enolase-like; domain 1
(252)
Homologous Superfamily
:
Enolase-like, N-terminal domain
(130)
Thermotoga maritima msb8. Organism_taxid: 243274. Strain: msb8 / dsm 3109 / jcm 10099.
(4)
1a
3dfyA01
A:3-115
1b
3dfyI01
I:3-115
1c
3dfyM01
M:3-115
1d
3dfyF01
F:3-115
1e
3dfyB01
B:3-115
1f
3dfyD01
D:3-115
1g
3dfyN01
N:3-115
1h
3dfyP01
P:3-115
1i
3dfyH01
H:3-115
1j
3dfyJ01
J:3-115
1k
3dfyL01
L:3-115
1l
3dfyO01
O:3-115
1m
3dfyE01
E:3-115
1n
3dfyG01
G:3-115
1o
3dfyK01
K:3-115
1p
3dfyC01
C:3-115
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Enolase superfamily
(142)
Thermotoga maritima msb8. Organism_taxid: 243274. Strain: msb8 / dsm 3109 / jcm 10099.
(4)
2a
3dfyB02
B:116-343
2b
3dfyE02
E:116-343
2c
3dfyF02
F:116-343
2d
3dfyG02
G:116-343
2e
3dfyH02
H:116-343
2f
3dfyJ02
J:116-343
2g
3dfyK02
K:116-343
2h
3dfyL02
L:116-343
2i
3dfyN02
N:116-343
2j
3dfyO02
O:116-343
2k
3dfyP02
P:116-343
2l
3dfyA02
A:116-343
2m
3dfyC02
C:116-343
2n
3dfyI02
I:116-343
2o
3dfyM02
M:116-343
2p
3dfyD02
D:116-343
[
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]
Pfam Domains
(0, 0)
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all PFAM domains
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Asym.Unit (866 KB)
Header - Asym.Unit
Biol.Unit 1 (433 KB)
Header - Biol.Unit 1
Biol.Unit 2 (435 KB)
Header - Biol.Unit 2
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