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3JW7
Asym. Unit
Info
Asym.Unit (464 KB)
Biol.Unit 1 (65 KB)
Biol.Unit 2 (66 KB)
Biol.Unit 3 (62 KB)
Biol.Unit 4 (62 KB)
Biol.Unit 5 (65 KB)
Biol.Unit 6 (64 KB)
Biol.Unit 7 (65 KB)
Biol.Unit 8 (66 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF DIPEPTIDE EPIMERASE FROM ENTEROCOCCUS FAECALIS V583 COMPLEXED WITH MG AND DIPEPTIDE L-ILE-L-TYR
Authors
:
A. A. Fedorov, E. V. Fedorov, H. J. Imker, A. Sakai, J. A. Gerlt, S. C. Almo
Date
:
18 Sep 09 (Deposition) - 11 Aug 10 (Release) - 23 May 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Biol. Unit 5: E (1x)
Biol. Unit 6: F (1x)
Biol. Unit 7: G (1x)
Biol. Unit 8: H (1x)
Keywords
:
Dipeptide Epimerase, Enolase Superfamily, Dipeptide L-Ile-L-Tyr, 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
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Hetero Components
(4, 32)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
1d: GLYCEROL (GOLd)
1e: GLYCEROL (GOLe)
1f: GLYCEROL (GOLf)
1g: GLYCEROL (GOLg)
1h: GLYCEROL (GOLh)
2a: ISOLEUCINE (ILEa)
2b: ISOLEUCINE (ILEb)
2c: ISOLEUCINE (ILEc)
2d: ISOLEUCINE (ILEd)
2e: ISOLEUCINE (ILEe)
2f: ISOLEUCINE (ILEf)
2g: ISOLEUCINE (ILEg)
2h: ISOLEUCINE (ILEh)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
3e: MAGNESIUM ION (MGe)
3f: MAGNESIUM ION (MGf)
3g: MAGNESIUM ION (MGg)
3h: MAGNESIUM ION (MGh)
4a: TYROSINE (TYRa)
4b: TYROSINE (TYRb)
4c: TYROSINE (TYRc)
4d: TYROSINE (TYRd)
4e: TYROSINE (TYRe)
4f: TYROSINE (TYRf)
4g: TYROSINE (TYRg)
4h: TYROSINE (TYRh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
8
Ligand/Ion
GLYCEROL
2
ILE
8
Mod. Amino Acid
ISOLEUCINE
3
MG
8
Ligand/Ion
MAGNESIUM ION
4
TYR
8
Mod. Amino Acid
TYROSINE
[
close Hetero Component info
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Sites
(32, 32)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PHE A:19 , THR A:134 , LYS A:161 , CYS A:292 , ASP A:318 , ASP A:320 , TYR A:356
BINDING SITE FOR RESIDUE ILE A 355
02
AC2
SOFTWARE
ILE A:21 , ILE A:26 , PHE A:53 , LYS A:159 , LYS A:161 , ASP A:189 , ASN A:191 , ASP A:240 , LYS A:264 , CYS A:292 , ALA A:294 , GLU A:295 , ILE A:355 , MG A:358 , HOH A:369
BINDING SITE FOR RESIDUE TYR A 356
03
AC3
SOFTWARE
LEU A:15 , PHE A:19 , ASP A:320 , ALA A:321 , PHE A:323 , GLY A:324 , HOH A:449 , HOH A:1068 , HOH A:1258
BINDING SITE FOR RESIDUE GOL A 357
04
AC4
SOFTWARE
LYS A:159 , ASP A:189 , GLU A:215 , ASP A:240 , TYR A:356 , HOH A:360
BINDING SITE FOR RESIDUE MG A 358
05
AC5
SOFTWARE
PHE B:19 , THR B:134 , LYS B:159 , LYS B:161 , CYS B:292 , ASP B:318 , ASP B:320 , TYR B:356
BINDING SITE FOR RESIDUE ILE B 355
06
AC6
SOFTWARE
ILE B:21 , ILE B:26 , PHE B:53 , LYS B:159 , LYS B:161 , ASP B:189 , ASN B:191 , ASP B:240 , LYS B:264 , CYS B:292 , ALA B:294 , GLU B:295 , ILE B:355 , MG B:358 , HOH B:369
BINDING SITE FOR RESIDUE TYR B 356
07
AC7
SOFTWARE
LEU B:15 , PHE B:19 , ASP B:320 , ALA B:321 , GLY B:324 , HOH B:644 , HOH B:1030 , HOH B:1082
BINDING SITE FOR RESIDUE GOL B 357
08
AC8
SOFTWARE
LYS B:159 , ASP B:189 , GLU B:215 , ASP B:240 , TYR B:356 , HOH B:359
BINDING SITE FOR RESIDUE MG B 358
09
AC9
SOFTWARE
PHE C:19 , THR C:134 , LYS C:161 , CYS C:292 , ASP C:318 , ASP C:320 , TYR C:356
BINDING SITE FOR RESIDUE ILE C 355
10
BC1
SOFTWARE
ILE C:21 , PHE C:53 , LYS C:159 , LYS C:161 , ASP C:189 , ASN C:191 , ASP C:240 , LYS C:264 , CYS C:292 , ALA C:294 , GLU C:295 , ILE C:355 , MG C:358 , HOH C:364
BINDING SITE FOR RESIDUE TYR C 356
11
BC2
SOFTWARE
LEU C:15 , PHE C:19 , ASP C:320 , ALA C:321 , PHE C:323 , GLY C:324 , HOH C:864
BINDING SITE FOR RESIDUE GOL C 357
12
BC3
SOFTWARE
LYS C:159 , ASP C:189 , GLU C:215 , ASP C:240 , TYR C:356 , HOH C:363
BINDING SITE FOR RESIDUE MG C 358
13
BC4
SOFTWARE
THR D:134 , LYS D:161 , CYS D:292 , ASP D:318 , ASP D:320 , TYR D:356
BINDING SITE FOR RESIDUE ILE D 355
14
BC5
SOFTWARE
ILE D:21 , ILE D:26 , PHE D:53 , LYS D:159 , LYS D:161 , ASP D:189 , ASN D:191 , ASP D:240 , LYS D:264 , CYS D:292 , ALA D:294 , GLU D:295 , ILE D:355 , MG D:358 , HOH D:397
BINDING SITE FOR RESIDUE TYR D 356
15
BC6
SOFTWARE
LEU D:15 , PHE D:19 , THR D:134 , ASP D:320 , ALA D:321 , GLY D:324 , HOH D:519
BINDING SITE FOR RESIDUE GOL D 357
16
BC7
SOFTWARE
LYS D:159 , ASP D:189 , GLU D:215 , ASP D:240 , TYR D:356 , HOH D:925
BINDING SITE FOR RESIDUE MG D 358
17
BC8
SOFTWARE
THR E:134 , LYS E:159 , LYS E:161 , CYS E:292 , ASP E:318 , ASP E:320 , TYR E:356
BINDING SITE FOR RESIDUE ILE E 355
18
BC9
SOFTWARE
ILE E:26 , PHE E:53 , LYS E:159 , LYS E:161 , ASP E:189 , ASN E:191 , GLU E:215 , ASP E:240 , LYS E:264 , CYS E:292 , ALA E:294 , GLU E:295 , ILE E:355 , MG E:358 , HOH E:387
BINDING SITE FOR RESIDUE TYR E 356
19
CC1
SOFTWARE
LEU E:15 , PHE E:19 , ASP E:320 , ALA E:321 , GLY E:324 , HOH E:414 , HOH E:459
BINDING SITE FOR RESIDUE GOL E 357
20
CC2
SOFTWARE
LYS E:159 , ASP E:189 , GLU E:215 , ASP E:240 , TYR E:356 , HOH E:368
BINDING SITE FOR RESIDUE MG E 358
21
CC3
SOFTWARE
THR F:134 , LYS F:159 , LYS F:161 , CYS F:292 , ASP F:318 , ASP F:320 , TYR F:356
BINDING SITE FOR RESIDUE ILE F 355
22
CC4
SOFTWARE
ILE F:21 , PHE F:53 , LYS F:159 , LYS F:161 , ASP F:189 , ASN F:191 , GLU F:215 , ASP F:240 , LYS F:264 , CYS F:292 , ALA F:294 , GLU F:295 , ILE F:355 , MG F:358 , HOH F:390
BINDING SITE FOR RESIDUE TYR F 356
23
CC5
SOFTWARE
LEU F:15 , PHE F:19 , ASP F:320 , ALA F:321 , PHE F:323 , GLY F:324 , HOH F:808 , HOH F:1032 , HOH F:2157
BINDING SITE FOR RESIDUE GOL F 357
24
CC6
SOFTWARE
ASP F:189 , GLU F:215 , ASP F:240 , TYR F:356 , HOH F:393
BINDING SITE FOR RESIDUE MG F 358
25
CC7
SOFTWARE
THR G:134 , LYS G:159 , LYS G:161 , CYS G:292 , ASP G:318 , ASP G:320 , TYR G:356
BINDING SITE FOR RESIDUE ILE G 355
26
CC8
SOFTWARE
ILE G:21 , ILE G:26 , PHE G:53 , LYS G:159 , LYS G:161 , ASP G:189 , ASN G:191 , ASP G:240 , LYS G:264 , CYS G:292 , ALA G:294 , GLU G:295 , ILE G:355 , MG G:358 , HOH G:406
BINDING SITE FOR RESIDUE TYR G 356
27
CC9
SOFTWARE
LEU G:15 , PHE G:19 , ASP G:320 , ALA G:321 , GLY G:324 , HOH G:719 , HOH G:1047 , HOH G:2223
BINDING SITE FOR RESIDUE GOL G 357
28
DC1
SOFTWARE
ASP G:189 , GLU G:215 , ASP G:240 , TYR G:356 , HOH G:384
BINDING SITE FOR RESIDUE MG G 358
29
DC2
SOFTWARE
THR H:134 , LYS H:159 , LYS H:161 , CYS H:292 , ASP H:318 , ASP H:320 , TYR H:356
BINDING SITE FOR RESIDUE ILE H 355
30
DC3
SOFTWARE
ILE H:26 , PHE H:53 , LYS H:159 , LYS H:161 , ASP H:189 , ASN H:191 , GLU H:215 , ASP H:240 , LYS H:264 , CYS H:292 , ALA H:294 , GLU H:295 , ILE H:355 , MG H:358 , HOH H:417
BINDING SITE FOR RESIDUE TYR H 356
31
DC4
SOFTWARE
LEU H:15 , PHE H:19 , ASP H:320 , ALA H:321 , PHE H:323 , GLY H:324 , HOH H:406 , HOH H:788 , HOH H:797
BINDING SITE FOR RESIDUE GOL H 357
32
DC5
SOFTWARE
LYS H:159 , ASP H:189 , GLU H:215 , ASP H:240 , TYR H:356 , HOH H:359
BINDING SITE FOR RESIDUE MG H 358
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 8)
Info
All PROSITE Patterns/Profiles
1: MR_MLE_2 (A:186-217,B:186-217,C:186-217,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.
HYEP_ENTFA
186-217
8
A:186-217
B:186-217
C:186-217
D:186-217
E:186-217
F:186-217
G:186-217
H:186-217
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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
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CATH Domains
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Pfam Domains
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Sorry, no Info available
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