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3RIT
Asym. Unit
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
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Hetero Components
(5, 44)
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
4
Ligand/Ion
PENTAETHYLENE GLYCOL
2
ARG
5
Mod. Amino Acid
ARGININE
3
DLY
5
Ligand/Ion
D-LYSINE
4
MG
5
Ligand/Ion
MAGNESIUM ION
5
SO4
25
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(44, 44)
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)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
42: EC6 (SOFTWARE)
43: EC7 (SOFTWARE)
44: EC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PRO A:231 , LYS A:232 , HOH A:387 , PRO B:231 , LYS B:232 , HOH B:395 , HOH B:957 , PRO C:231 , LYS C:232 , HOH C:388
BINDING SITE FOR RESIDUE SO4 A 357
02
AC2
SOFTWARE
GLY A:246 , PRO A:247 , ALA A:248 , HOH A:374 , HOH A:540 , HOH A:694 , HOH A:1017
BINDING SITE FOR RESIDUE SO4 A 358
03
AC3
SOFTWARE
ARG A:235 , HOH A:662 , PRO B:257 , HOH B:424 , HOH B:957 , ARG C:235 , HOH C:390
BINDING SITE FOR RESIDUE SO4 A 359
04
AC4
SOFTWARE
ARG A:87 , ARG A:278 , HOH A:407 , HOH A:1034 , LEU C:123 , ALA C:311 , PRO C:313
BINDING SITE FOR RESIDUE SO4 A 360
05
AC5
SOFTWARE
LYS A:2 , ARG A:77 , ASP A:78 , HOH A:457
BINDING SITE FOR RESIDUE SO4 A 361
06
AC6
SOFTWARE
THR A:224 , HOH A:405 , HOH A:1014 , HOH A:1040 , HOH A:1041 , THR B:224 , ARG B:228
BINDING SITE FOR RESIDUE SO4 A 362
07
AC7
SOFTWARE
TYR A:19 , THR A:135 , LYS A:160 , CYS A:294 , ASP A:296 , ASP A:319 , ASP A:321 , DLY A:364 , HOH A:403 , HOH A:908
BINDING SITE FOR RESIDUE ARG A 363
08
AC8
SOFTWARE
GLU A:51 , LYS A:160 , LYS A:162 , ASP A:190 , ASN A:192 , GLU A:216 , ASP A:241 , GLU A:242 , LYS A:266 , ARG A:363 , MG A:365
BINDING SITE FOR RESIDUE DLY A 364
09
AC9
SOFTWARE
ASP A:190 , GLU A:216 , ASP A:241 , GLU A:242 , DLY A:364
BINDING SITE FOR RESIDUE MG A 365
10
BC1
SOFTWARE
HIS A:53 , VAL A:54 , HIS B:53 , VAL B:54 , THR B:55 , GLY B:56
BINDING SITE FOR RESIDUE 1PE A 366
11
BC2
SOFTWARE
GLY B:246 , PRO B:247 , ALA B:248 , HOH B:364 , HOH B:399 , HOH B:497
BINDING SITE FOR RESIDUE SO4 B 357
12
BC3
SOFTWARE
ARG B:77 , ASP B:78 , HOH B:376
BINDING SITE FOR RESIDUE SO4 B 358
13
BC4
SOFTWARE
ARG B:87 , LEU B:123 , ARG B:278 , ALA B:311 , HOH B:859
BINDING SITE FOR RESIDUE SO4 B 359
14
BC5
SOFTWARE
ARG A:157 , ARG B:157 , HOH B:384
BINDING SITE FOR RESIDUE SO4 B 360
15
BC6
SOFTWARE
TYR B:19 , THR B:135 , LYS B:160 , LYS B:162 , CYS B:294 , ASP B:296 , ASP B:319 , ASP B:321 , ASP B:325 , DLY B:362
BINDING SITE FOR RESIDUE ARG B 361
16
BC7
SOFTWARE
TYR B:19 , ARG B:24 , GLU B:51 , LYS B:160 , LYS B:162 , ASP B:190 , ASN B:192 , GLU B:216 , ASP B:241 , GLU B:242 , LYS B:266 , MET B:295 , ARG B:361 , MG B:363
BINDING SITE FOR RESIDUE DLY B 362
17
BC8
SOFTWARE
ASP B:190 , ASN B:192 , GLU B:216 , ASP B:241 , GLU B:242 , DLY B:362
BINDING SITE FOR RESIDUE MG B 363
18
BC9
SOFTWARE
GLY C:246 , PRO C:247 , ALA C:248 , HOH C:368 , HOH C:614
BINDING SITE FOR RESIDUE SO4 C 357
19
CC1
SOFTWARE
LEU A:123 , ALA A:311 , PRO A:313 , ARG C:87 , ARG C:278 , HOH C:1030
BINDING SITE FOR RESIDUE SO4 C 358
20
CC2
SOFTWARE
ARG C:77 , ASP C:78 , HOH C:400 , HOH C:625
BINDING SITE FOR RESIDUE SO4 C 359
21
CC3
SOFTWARE
THR C:224 , ARG C:228 , HOH C:1026 , HOH C:1033
BINDING SITE FOR RESIDUE SO4 C 360
22
CC4
SOFTWARE
TYR C:19 , THR C:135 , LYS C:160 , CYS C:294 , MET C:295 , ASP C:296 , ASP C:319 , ASP C:321 , GLY C:322 , DLY C:362
BINDING SITE FOR RESIDUE ARG C 361
23
CC5
SOFTWARE
GLU C:51 , LYS C:160 , LYS C:162 , ASP C:190 , ASN C:192 , GLU C:216 , ASP C:241 , LYS C:266 , MET C:295 , ARG C:361 , MG C:363
BINDING SITE FOR RESIDUE DLY C 362
24
CC6
SOFTWARE
ASP C:190 , GLU C:216 , ASP C:241 , GLU C:242 , DLY C:362
BINDING SITE FOR RESIDUE MG C 363
25
CC7
SOFTWARE
VAL C:54 , THR C:55
BINDING SITE FOR RESIDUE 1PE C 364
26
CC8
SOFTWARE
GLY D:246 , PRO D:247 , ALA D:248 , HOH D:382 , HOH D:622
BINDING SITE FOR RESIDUE SO4 D 357
27
CC9
SOFTWARE
ARG D:87 , ARG D:278 , HOH D:1037 , LEU E:123 , ALA E:311
BINDING SITE FOR RESIDUE SO4 D 358
28
DC1
SOFTWARE
LYS D:2 , ARG D:77 , ASP D:78
BINDING SITE FOR RESIDUE SO4 D 359
29
DC2
SOFTWARE
PRO D:231 , LYS D:232 , HOH D:406
BINDING SITE FOR RESIDUE SO4 D 360
30
DC3
SOFTWARE
ARG D:235
BINDING SITE FOR RESIDUE SO4 D 361
31
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
32
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
33
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
34
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
35
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
36
DC9
SOFTWARE
GLY E:246 , PRO E:247 , ALA E:248 , HOH E:433
BINDING SITE FOR RESIDUE SO4 E 357
37
EC1
SOFTWARE
PRO E:231 , LYS E:232
BINDING SITE FOR RESIDUE SO4 E 358
38
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
39
EC3
SOFTWARE
ARG E:77 , ASP E:78 , HOH E:378
BINDING SITE FOR RESIDUE SO4 E 360
40
EC4
SOFTWARE
ARG E:235
BINDING SITE FOR RESIDUE SO4 E 361
41
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
42
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
43
EC7
SOFTWARE
ASP E:190 , GLU E:216 , ASP E:241 , GLU E:242 , DLY E:363
BINDING SITE FOR RESIDUE MG E 364
44
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
[
close Site info
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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]
PROSITE Patterns/Profiles
(1, 5)
Info
All PROSITE Patterns/Profiles
1: MR_MLE_2 (A:187-218,B:187-218,C:187-218,D:18...)
;
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
5
A:187-218
B:187-218
C:187-218
D:187-218
E:187-218
[
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Exons
(0, 0)
Info
All Exons
View:
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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, 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)
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(
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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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Sorry, no Info available
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Pfam Domains
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all PFAM domains
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Sorry, no Info available
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