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3Q4D
Biol. Unit 6
Info
Asym.Unit (525 KB)
Biol.Unit 1 (65 KB)
Biol.Unit 2 (66 KB)
Biol.Unit 3 (66 KB)
Biol.Unit 4 (65 KB)
Biol.Unit 5 (65 KB)
Biol.Unit 6 (65 KB)
Biol.Unit 7 (65 KB)
Biol.Unit 8 (65 KB)
Biol.Unit 9 (65 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF DIPEPTIDE EPIMERASE FROM CYTOPHAGA HUTCHINSONII COMPLEXED WITH MG AND DIPEPTIDE D-ALA-L-ALA
Authors
:
T. Lukk, J. A. Gerlt, S. K. Nair
Date
:
23 Dec 10 (Deposition) - 16 Feb 11 (Release) - 28 Mar 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I
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)
Biol. Unit 9: I (1x)
Keywords
:
(Beta/Alpha)8-Barrel, 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
(2, 2)
Info
All Hetero Components
1a: ALANINE (ALAa)
1b: ALANINE (ALAb)
1c: ALANINE (ALAc)
1d: ALANINE (ALAd)
1e: ALANINE (ALAe)
1f: ALANINE (ALAf)
1g: ALANINE (ALAg)
1h: ALANINE (ALAh)
1i: ALANINE (ALAi)
2a: D-ALANINE (DALa)
2b: D-ALANINE (DALb)
2c: D-ALANINE (DALc)
2d: D-ALANINE (DALd)
2e: D-ALANINE (DALe)
2f: D-ALANINE (DALf)
2g: D-ALANINE (DALg)
2h: D-ALANINE (DALh)
2i: D-ALANINE (DALi)
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)
3i: MAGNESIUM ION (MGi)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ALA
1
Mod. Amino Acid
ALANINE
2
DAL
1
Ligand/Ion
D-ALANINE
3
MG
-1
Ligand/Ion
MAGNESIUM ION
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Sites
(3, 3)
Info
All Sites
1: BC7 (SOFTWARE)
2: BC8 (SOFTWARE)
3: BC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
BC7
SOFTWARE
ASP F:190 , ASN F:192 , GLU F:216 , ASP F:241 , GLU F:242 , ALA F:2481
BINDING SITE FOR RESIDUE MG F 1606
2
BC8
SOFTWARE
THR F:135 , LYS F:160 , LYS F:162 , GLY F:293 , ASP F:318 , ASP F:320 , ALA F:2481
BINDING SITE FOR RESIDUE DAL F 2480
3
BC9
SOFTWARE
LYS F:160 , LYS F:162 , ASP F:190 , GLU F:216 , ASP F:241 , LYS F:265 , GLY F:293 , ASP F:318 , MG F:1606 , DAL F:2480
BINDING SITE FOR RESIDUE ALA F 2481
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(, 0)
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Exons
(0, 0)
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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, 18)
Info
All SCOP Domains
1a: SCOP_d3q4da1 (A:1-124)
1b: SCOP_d3q4db1 (B:1-124)
1c: SCOP_d3q4dc1 (C:1-124)
1d: SCOP_d3q4dd1 (D:1-124)
1e: SCOP_d3q4de1 (E:1-124)
1f: SCOP_d3q4df1 (F:1-124)
1g: SCOP_d3q4dg1 (G:1-124)
1h: SCOP_d3q4dh1 (H:1-124)
1i: SCOP_d3q4di1 (I:1-124)
2a: SCOP_d3q4da2 (A:125-368)
2b: SCOP_d3q4db2 (B:125-368)
2c: SCOP_d3q4dc2 (C:125-368)
2d: SCOP_d3q4dd2 (D:125-368)
2e: SCOP_d3q4de2 (E:125-368)
2f: SCOP_d3q4df2 (F:125-368)
2g: SCOP_d3q4dg2 (G:125-368)
2h: SCOP_d3q4dh2 (H:125-368)
2i: SCOP_d3q4di2 (I:125-368)
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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)
Cytophaga hutchinsonii [TaxId: 269798]
(2)
1a
d3q4da1
A:1-124
1b
d3q4db1
B:1-124
1c
d3q4dc1
C:1-124
1d
d3q4dd1
D:1-124
1e
d3q4de1
E:1-124
1f
d3q4df1
F:1-124
1g
d3q4dg1
G:1-124
1h
d3q4dh1
H:1-124
1i
d3q4di1
I:1-124
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)
Cytophaga hutchinsonii [TaxId: 269798]
(2)
2a
d3q4da2
A:125-368
2b
d3q4db2
B:125-368
2c
d3q4dc2
C:125-368
2d
d3q4dd2
D:125-368
2e
d3q4de2
E:125-368
2f
d3q4df2
F:125-368
2g
d3q4dg2
G:125-368
2h
d3q4dh2
H:125-368
2i
d3q4di2
I:125-368
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CATH Domains
(0, 0)
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all CATH domains
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Pfam Domains
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Chain F
Asymmetric Unit 1
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select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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Show PDB file:
Asym.Unit (525 KB)
Header - Asym.Unit
Biol.Unit 1 (65 KB)
Header - Biol.Unit 1
Biol.Unit 2 (66 KB)
Header - Biol.Unit 2
Biol.Unit 3 (66 KB)
Header - Biol.Unit 3
Biol.Unit 4 (65 KB)
Header - Biol.Unit 4
Biol.Unit 5 (65 KB)
Header - Biol.Unit 5
Biol.Unit 6 (65 KB)
Header - Biol.Unit 6
Biol.Unit 7 (65 KB)
Header - Biol.Unit 7
Biol.Unit 8 (65 KB)
Header - Biol.Unit 8
Biol.Unit 9 (65 KB)
Header - Biol.Unit 9
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