PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
3Q4D
Asym. Unit
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)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(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
[
close entry info
]
Hetero Components
(3, 27)
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
9
Mod. Amino Acid
ALANINE
2
DAL
9
Ligand/Ion
D-ALANINE
3
MG
9
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(27, 27)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:190 , GLU A:216 , ASP A:241 , ALA A:2473
BINDING SITE FOR RESIDUE MG A 1602
02
AC2
SOFTWARE
PHE A:19 , THR A:135 , LYS A:162 , GLY A:293 , PHE A:294 , ASP A:318 , ASP A:320 , THR A:321 , ALA A:2473
BINDING SITE FOR RESIDUE DAL A 2472
03
AC3
SOFTWARE
LYS A:160 , LYS A:162 , ASP A:190 , ASN A:192 , ASP A:241 , LYS A:265 , GLY A:293 , ASP A:318 , MG A:1602 , DAL A:2472
BINDING SITE FOR RESIDUE ALA A 2473
04
AC4
SOFTWARE
ASP B:190 , ASN B:192 , GLU B:216 , ASP B:241 , GLU B:242 , ALA B:2471
BINDING SITE FOR RESIDUE MG B 1601
05
AC5
SOFTWARE
PHE B:19 , THR B:135 , LYS B:162 , GLY B:293 , PHE B:294 , ASP B:318 , ASP B:320 , THR B:321 , ALA B:2471
BINDING SITE FOR RESIDUE DAL B 2470
06
AC6
SOFTWARE
LYS B:160 , LYS B:162 , ASP B:190 , ASN B:192 , GLU B:216 , ASP B:241 , LYS B:265 , GLY B:293 , ASP B:318 , HOH B:370 , MG B:1601 , DAL B:2470
BINDING SITE FOR RESIDUE ALA B 2471
07
AC7
SOFTWARE
ASP C:190 , ASN C:192 , GLU C:216 , ASP C:241 , GLU C:242 , ALA C:2475
BINDING SITE FOR RESIDUE MG C 1603
08
AC8
SOFTWARE
PHE C:19 , THR C:135 , LYS C:162 , GLY C:293 , PHE C:294 , ASP C:318 , ASP C:320 , ALA C:2475
BINDING SITE FOR RESIDUE DAL C 2474
09
AC9
SOFTWARE
LYS C:160 , LYS C:162 , ASP C:190 , ASN C:192 , GLU C:216 , ASP C:241 , LYS C:265 , GLY C:293 , ASP C:318 , MG C:1603 , DAL C:2474
BINDING SITE FOR RESIDUE ALA C 2475
10
BC1
SOFTWARE
ASP D:190 , ASN D:192 , GLU D:216 , ASP D:241 , GLU D:242 , ALA D:2477
BINDING SITE FOR RESIDUE MG D 1604
11
BC2
SOFTWARE
PHE D:19 , THR D:135 , LYS D:162 , GLY D:293 , ASP D:318 , ASP D:320 , THR D:321 , ALA D:2477
BINDING SITE FOR RESIDUE DAL D 2476
12
BC3
SOFTWARE
LYS D:160 , LYS D:162 , ASP D:190 , ASP D:241 , LYS D:265 , GLY D:293 , ASP D:318 , MG D:1604 , DAL D:2476
BINDING SITE FOR RESIDUE ALA D 2477
13
BC4
SOFTWARE
ASP E:190 , ASN E:192 , GLU E:216 , ASP E:241 , GLU E:242 , ALA E:2479
BINDING SITE FOR RESIDUE MG E 1605
14
BC5
SOFTWARE
PHE E:19 , THR E:135 , LYS E:160 , LYS E:162 , GLY E:293 , ASP E:318 , ASP E:320 , ALA E:2479
BINDING SITE FOR RESIDUE DAL E 2478
15
BC6
SOFTWARE
LYS E:160 , LYS E:162 , ASP E:190 , ASN E:192 , GLU E:216 , ASP E:241 , LYS E:265 , GLY E:293 , MG E:1605 , DAL E:2478
BINDING SITE FOR RESIDUE ALA E 2479
16
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
17
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
18
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
19
CC1
SOFTWARE
ASP G:190 , ASN G:192 , GLU G:216 , ASP G:241 , GLU G:242 , ALA G:2483
BINDING SITE FOR RESIDUE MG G 1607
20
CC2
SOFTWARE
PHE G:19 , THR G:135 , LYS G:162 , GLY G:293 , ASP G:318 , ASP G:320 , ALA G:2483
BINDING SITE FOR RESIDUE DAL G 2482
21
CC3
SOFTWARE
LYS G:160 , LYS G:162 , ASP G:190 , ASN G:192 , GLU G:216 , ASP G:241 , LYS G:265 , GLY G:293 , PHE G:294 , MG G:1607 , DAL G:2482
BINDING SITE FOR RESIDUE ALA G 2483
22
CC4
SOFTWARE
ASP H:190 , ASN H:192 , GLU H:216 , ASP H:241 , GLU H:242 , ALA H:2485
BINDING SITE FOR RESIDUE MG H 1608
23
CC5
SOFTWARE
PHE H:19 , THR H:135 , LYS H:162 , GLY H:293 , ASP H:318 , ASP H:320 , ALA H:2485
BINDING SITE FOR RESIDUE DAL H 2484
24
CC6
SOFTWARE
LYS H:160 , LYS H:162 , ASP H:190 , ASN H:192 , GLU H:216 , ASP H:241 , LYS H:265 , GLY H:293 , MG H:1608 , DAL H:2484
BINDING SITE FOR RESIDUE ALA H 2485
25
CC7
SOFTWARE
ASP I:190 , GLU I:216 , ASP I:241 , ALA I:2487
BINDING SITE FOR RESIDUE MG I 1609
26
CC8
SOFTWARE
PHE I:19 , THR I:135 , LYS I:162 , GLY I:293 , ASP I:318 , ASP I:320 , ALA I:2487
BINDING SITE FOR RESIDUE DAL I 2486
27
CC9
SOFTWARE
LYS I:160 , LYS I:162 , ASP I:190 , ASN I:192 , GLU I:216 , ASP I:241 , LYS I:265 , GLY I:293 , MG I:1609 , DAL I:2486
BINDING SITE FOR RESIDUE ALA I 2487
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
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, 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)
View:
Select:
Label:
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)
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
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Chain E
Chain F
Chain G
Chain H
Chain I
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
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
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
3Q4D
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help