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3RIT
Biol. Unit 3
Info
Asym.Unit (300 KB)
Biol.Unit 1 (121 KB)
Biol.Unit 2 (122 KB)
Biol.Unit 3 (120 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF DIPEPTIDE EPIMERASE FROM METHYLOCOCCUS CAPSULATUS COMPLEXED WITH MG AND DIPEPTIDE L-ARG-D-LYS
Authors
:
T. Lukk, A. Sakai, L. Song, J. A. Gerlt, S. K. Nair
Date
:
14 Apr 11 (Deposition) - 27 Apr 11 (Release) - 28 Mar 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A,B,C,D,E
Biol. Unit 1: A,C (1x)
Biol. Unit 2: B (2x)
Biol. Unit 3: D,E (1x)
Keywords
:
Tim Barrel, Chloromuconate Cycloisomerase, Isomerase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Lukk, A. Sakai, C. Kalyanaraman, S. D. Brown, H. J. Imker, L. Song, A. A. Fedorov, E. V. Fedorov, R. Toro, B. Hillerich, R. Seidel, Y. Patskovsky, M. W. Vetting, S. K. Nair, P. C. Babbitt, S. C. Almo, J. A. Gerlt, M. P. Jacobson
Homology Models Guide Discovery Of Diverse Enzyme Specificities Among Dipeptide Epimerases In The Enolase Superfamily.
Proc. Natl. Acad. Sci. Usa V. 109 4122 2012
[
close entry info
]
Hetero Components
(4, 17)
Info
All Hetero Components
1a: PENTAETHYLENE GLYCOL (1PEa)
1b: PENTAETHYLENE GLYCOL (1PEb)
1c: PENTAETHYLENE GLYCOL (1PEc)
1d: PENTAETHYLENE GLYCOL (1PEd)
2a: ARGININE (ARGa)
2b: ARGININE (ARGb)
2c: ARGININE (ARGc)
2d: ARGININE (ARGd)
2e: ARGININE (ARGe)
3a: D-LYSINE (DLYa)
3b: D-LYSINE (DLYb)
3c: D-LYSINE (DLYc)
3d: D-LYSINE (DLYd)
3e: D-LYSINE (DLYe)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
4c: MAGNESIUM ION (MGc)
4d: MAGNESIUM ION (MGd)
4e: MAGNESIUM ION (MGe)
5a: SULFATE ION (SO4a)
5b: SULFATE ION (SO4b)
5c: SULFATE ION (SO4c)
5d: SULFATE ION (SO4d)
5e: SULFATE ION (SO4e)
5f: SULFATE ION (SO4f)
5g: SULFATE ION (SO4g)
5h: SULFATE ION (SO4h)
5i: SULFATE ION (SO4i)
5j: SULFATE ION (SO4j)
5k: SULFATE ION (SO4k)
5l: SULFATE ION (SO4l)
5m: SULFATE ION (SO4m)
5n: SULFATE ION (SO4n)
5o: SULFATE ION (SO4o)
5p: SULFATE ION (SO4p)
5q: SULFATE ION (SO4q)
5r: SULFATE ION (SO4r)
5s: SULFATE ION (SO4s)
5t: SULFATE ION (SO4t)
5u: SULFATE ION (SO4u)
5v: SULFATE ION (SO4v)
5w: SULFATE ION (SO4w)
5x: SULFATE ION (SO4x)
5y: SULFATE ION (SO4y)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
1PE
2
Ligand/Ion
PENTAETHYLENE GLYCOL
2
ARG
2
Mod. Amino Acid
ARGININE
3
DLY
2
Ligand/Ion
D-LYSINE
4
MG
-1
Ligand/Ion
MAGNESIUM ION
5
SO4
11
Ligand/Ion
SULFATE ION
[
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]
Sites
(19, 19)
Info
All Sites
01: CC8 (SOFTWARE)
02: CC9 (SOFTWARE)
03: DC1 (SOFTWARE)
04: DC2 (SOFTWARE)
05: DC3 (SOFTWARE)
06: DC4 (SOFTWARE)
07: DC5 (SOFTWARE)
08: DC6 (SOFTWARE)
09: DC7 (SOFTWARE)
10: DC8 (SOFTWARE)
11: DC9 (SOFTWARE)
12: EC1 (SOFTWARE)
13: EC2 (SOFTWARE)
14: EC3 (SOFTWARE)
15: EC4 (SOFTWARE)
16: EC5 (SOFTWARE)
17: EC6 (SOFTWARE)
18: EC7 (SOFTWARE)
19: EC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
CC8
SOFTWARE
GLY D:246 , PRO D:247 , ALA D:248 , HOH D:382 , HOH D:622
BINDING SITE FOR RESIDUE SO4 D 357
02
CC9
SOFTWARE
ARG D:87 , ARG D:278 , HOH D:1037 , LEU E:123 , ALA E:311
BINDING SITE FOR RESIDUE SO4 D 358
03
DC1
SOFTWARE
LYS D:2 , ARG D:77 , ASP D:78
BINDING SITE FOR RESIDUE SO4 D 359
04
DC2
SOFTWARE
PRO D:231 , LYS D:232 , HOH D:406
BINDING SITE FOR RESIDUE SO4 D 360
05
DC3
SOFTWARE
ARG D:235
BINDING SITE FOR RESIDUE SO4 D 361
06
DC4
SOFTWARE
THR D:224 , ARG D:228 , HOH D:1016 , HOH D:1027 , HOH D:1028 , HOH D:1029 , THR E:224 , HOH E:623
BINDING SITE FOR RESIDUE SO4 D 362
07
DC5
SOFTWARE
TYR D:19 , THR D:135 , LYS D:162 , CYS D:294 , ASP D:296 , ASP D:319 , ASP D:321 , ASP D:325 , DLY D:364
BINDING SITE FOR RESIDUE ARG D 363
08
DC6
SOFTWARE
ILE D:21 , GLU D:51 , LYS D:160 , LYS D:162 , ASP D:190 , ASN D:192 , GLU D:216 , ASP D:241 , ASN D:264 , LYS D:266 , MET D:295 , ARG D:363 , MG D:365
BINDING SITE FOR RESIDUE DLY D 364
09
DC7
SOFTWARE
ASP D:190 , ASN D:192 , GLU D:216 , ASP D:241 , GLU D:242 , DLY D:364
BINDING SITE FOR RESIDUE MG D 365
10
DC8
SOFTWARE
THR D:55 , HIS E:53 , VAL E:54 , THR E:55 , LEU E:245 , 1PE E:365
BINDING SITE FOR RESIDUE 1PE D 366
11
DC9
SOFTWARE
GLY E:246 , PRO E:247 , ALA E:248 , HOH E:433
BINDING SITE FOR RESIDUE SO4 E 357
12
EC1
SOFTWARE
PRO E:231 , LYS E:232
BINDING SITE FOR RESIDUE SO4 E 358
13
EC2
SOFTWARE
LEU D:123 , ALA D:311 , PRO D:313 , ARG E:87 , ARG E:278 , HOH E:369 , HOH E:1035
BINDING SITE FOR RESIDUE SO4 E 359
14
EC3
SOFTWARE
ARG E:77 , ASP E:78 , HOH E:378
BINDING SITE FOR RESIDUE SO4 E 360
15
EC4
SOFTWARE
ARG E:235
BINDING SITE FOR RESIDUE SO4 E 361
16
EC5
SOFTWARE
TYR E:19 , THR E:135 , LYS E:162 , CYS E:294 , ASP E:296 , ASP E:319 , ASP E:321 , ASP E:325 , DLY E:363
BINDING SITE FOR RESIDUE ARG E 362
17
EC6
SOFTWARE
TYR E:19 , ILE E:21 , GLU E:51 , LYS E:160 , LYS E:162 , ASP E:190 , ASN E:192 , GLU E:216 , ASP E:241 , LYS E:266 , MET E:295 , ARG E:362 , MG E:364
BINDING SITE FOR RESIDUE DLY E 363
18
EC7
SOFTWARE
ASP E:190 , GLU E:216 , ASP E:241 , GLU E:242 , DLY E:363
BINDING SITE FOR RESIDUE MG E 364
19
EC8
SOFTWARE
HIS D:53 , VAL D:54 , THR D:55 , GLY D:56 , LEU D:245 , 1PE D:366 , GLY E:56
BINDING SITE FOR RESIDUE 1PE E 365
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: MR_MLE_2 (D:187-218,E:187-218)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
MR_MLE_2
PS00909
Mandelate racemase / muconate lactonizing enzyme family signature 2.
KRDE_METCA
187-218
2
-
-
-
D:187-218
E:187-218
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 10)
Info
All SCOP Domains
1a: SCOP_d3rita1 (A:1-125)
1b: SCOP_d3rite1 (E:1-125)
1c: SCOP_d3ritb1 (B:1-125)
1d: SCOP_d3ritc1 (C:1-125)
1e: SCOP_d3ritd1 (D:1-125)
2a: SCOP_d3rita2 (A:126-354)
2b: SCOP_d3rite2 (E:126-354)
2c: SCOP_d3ritb2 (B:126-354)
2d: SCOP_d3ritc2 (C:126-354)
2e: SCOP_d3ritd2 (D:126-354)
View:
Select:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
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)
Methylococcus capsulatus [TaxId: 414]
(2)
1a
d3rita1
A:1-125
1b
d3rite1
E:1-125
1c
d3ritb1
B:1-125
1d
d3ritc1
C:1-125
1e
d3ritd1
D:1-125
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)
Methylococcus capsulatus [TaxId: 414]
(2)
2a
d3rita2
A:126-354
2b
d3rite2
E:126-354
2c
d3ritb2
B:126-354
2d
d3ritc2
C:126-354
2e
d3ritd2
D:126-354
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
[
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Pfam Domains
(0, 0)
Info
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Sorry, no Info available
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Protein & NOT Site
Protein & NOT PROSITE
Chain D
Chain E
Asymmetric Unit 1
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