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.
1TKK
Asym. Unit
Info
Asym.Unit (473 KB)
Biol.Unit 1 (466 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
THE STRUCTURE OF A SUBSTRATE-LIGANDED COMPLEX OF THE L-ALA-D/L-GLU EPIMERASE FROM BACILLUS SUBTILIS
Authors
:
V. A. Klenchin, D. M. Schmidt, J. A. Gerlt, I. Rayment
Date
:
08 Jun 04 (Deposition) - 31 Aug 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D,E,F,G,H (1x)
Keywords
:
Epimerase, Enolase Super Family, , Isomerase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
V. A. Klenchin, D. M. Schmidt, J. A. Gerlt, I. Rayment
Evolution Of Enzymatic Activities In The Enolase Superfamily: Structure Of A Substrate-Liganded Complex Of The L-Ala-D/L-Glu Epimerase From Bacillus Subtilis(, ).
Biochemistry V. 43 10370 2004
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 24)
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)
2a: GLUTAMIC ACID (GLUa)
2b: GLUTAMIC ACID (GLUb)
2c: GLUTAMIC ACID (GLUc)
2d: GLUTAMIC ACID (GLUd)
2e: GLUTAMIC ACID (GLUe)
2f: GLUTAMIC ACID (GLUf)
2g: GLUTAMIC ACID (GLUg)
2h: GLUTAMIC ACID (GLUh)
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)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ALA
8
Mod. Amino Acid
ALANINE
2
GLU
8
Mod. Amino Acid
GLUTAMIC ACID
3
MG
8
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(24, 24)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LYS A:160 , ASP A:191 , GLU A:219 , ASP A:244 , GLU A:2471 , HOH A:2472
BINDING SITE FOR RESIDUE MG A 1601
02
AC2
SOFTWARE
LYS B:160 , ASP B:191 , GLU B:219 , ASP B:244 , GLU B:2473 , HOH B:2474
BINDING SITE FOR RESIDUE MG B 1602
03
AC3
SOFTWARE
LYS C:160 , ASP C:191 , GLU C:219 , ASP C:244 , GLU C:2475 , HOH C:2476
BINDING SITE FOR RESIDUE MG C 1603
04
AC4
SOFTWARE
ASP D:191 , ASN D:193 , GLU D:219 , ASP D:244 , GLU D:2477 , HOH D:2478
BINDING SITE FOR RESIDUE MG D 1604
05
AC5
SOFTWARE
ASP E:191 , GLU E:219 , ASP E:244 , GLU E:2479 , HOH E:2480
BINDING SITE FOR RESIDUE MG E 1605
06
AC6
SOFTWARE
ASP F:191 , GLU F:219 , ASP F:244 , GLU F:2481 , HOH F:2482
BINDING SITE FOR RESIDUE MG F 1606
07
AC7
SOFTWARE
LYS G:160 , ASP G:191 , GLU G:219 , ASP G:244 , GLU G:2483 , HOH G:2484
BINDING SITE FOR RESIDUE MG G 1607
08
AC8
SOFTWARE
LYS H:160 , ASP H:191 , GLU H:219 , ASP H:244 , GLU H:2485 , HOH H:2486
BINDING SITE FOR RESIDUE MG H 1608
09
AC9
SOFTWARE
PHE A:19 , THR A:135 , LYS A:160 , LYS A:162 , ASP A:321 , ASP A:323 , GLU A:2471
BINDING SITE FOR RESIDUE ALA A 2470
10
BC1
SOFTWARE
PHE A:19 , ARG A:24 , ILE A:54 , LYS A:160 , LYS A:162 , ASP A:191 , ASP A:244 , LYS A:268 , SER A:296 , MET A:297 , ILE A:298 , MG A:1601 , ALA A:2470 , HOH A:2541 , HOH A:2577
BINDING SITE FOR RESIDUE GLU A 2471
11
BC2
SOFTWARE
PHE B:19 , THR B:135 , LYS B:160 , LYS B:162 , ASP B:321 , ASP B:323 , GLU B:2473
BINDING SITE FOR RESIDUE ALA B 2472
12
BC3
SOFTWARE
PHE B:19 , ARG B:24 , ILE B:54 , LYS B:160 , LYS B:162 , ASP B:191 , GLU B:219 , ASP B:244 , LYS B:268 , SER B:296 , ILE B:298 , MG B:1602 , ALA B:2472 , HOH B:2484 , HOH B:2510
BINDING SITE FOR RESIDUE GLU B 2473
13
BC4
SOFTWARE
THR C:135 , LYS C:160 , LYS C:162 , ASP C:321 , ASP C:323 , GLU C:2475
BINDING SITE FOR RESIDUE ALA C 2474
14
BC5
SOFTWARE
PHE C:19 , ARG C:24 , ILE C:54 , LYS C:160 , LYS C:162 , ASP C:191 , ASP C:244 , LYS C:268 , SER C:296 , MET C:297 , ILE C:298 , MG C:1603 , ALA C:2474 , HOH C:2479
BINDING SITE FOR RESIDUE GLU C 2475
15
BC6
SOFTWARE
PHE D:19 , THR D:135 , LYS D:160 , LYS D:162 , ASP D:321 , ASP D:323 , GLU D:2477
BINDING SITE FOR RESIDUE ALA D 2476
16
BC7
SOFTWARE
PHE D:19 , ARG D:24 , ILE D:54 , LYS D:160 , LYS D:162 , ASP D:191 , ASP D:244 , LYS D:268 , SER D:296 , MET D:297 , ILE D:298 , MG D:1604 , ALA D:2476 , HOH D:2521 , HOH D:2530
BINDING SITE FOR RESIDUE GLU D 2477
17
BC8
SOFTWARE
THR E:135 , LYS E:160 , LYS E:162 , ASP E:321 , ASP E:323 , GLU E:2479
BINDING SITE FOR RESIDUE ALA E 2478
18
BC9
SOFTWARE
PHE E:19 , ARG E:24 , LYS E:160 , LYS E:162 , ASP E:244 , LYS E:268 , SER E:296 , ILE E:298 , MG E:1605 , ALA E:2478 , HOH E:2526 , HOH E:2528
BINDING SITE FOR RESIDUE GLU E 2479
19
CC1
SOFTWARE
PHE F:19 , THR F:135 , LYS F:160 , LYS F:162 , ASP F:321 , ASP F:323 , GLU F:2481
BINDING SITE FOR RESIDUE ALA F 2480
20
CC2
SOFTWARE
PHE F:19 , ARG F:24 , ILE F:54 , LYS F:160 , LYS F:162 , ASP F:191 , ASP F:244 , LYS F:268 , SER F:296 , MET F:297 , ILE F:298 , MG F:1606 , ALA F:2480 , HOH F:2531 , HOH F:2539
BINDING SITE FOR RESIDUE GLU F 2481
21
CC3
SOFTWARE
PHE G:19 , THR G:135 , LYS G:160 , LYS G:162 , SER G:296 , ASP G:321 , ASP G:323 , GLU G:2483
BINDING SITE FOR RESIDUE ALA G 2482
22
CC4
SOFTWARE
PHE G:19 , ARG G:24 , ILE G:54 , LYS G:160 , LYS G:162 , ASP G:191 , ASP G:244 , LYS G:268 , SER G:296 , MET G:297 , ILE G:298 , MG G:1607 , ALA G:2482 , HOH G:2519 , HOH G:2520
BINDING SITE FOR RESIDUE GLU G 2483
23
CC5
SOFTWARE
PHE H:19 , THR H:135 , LYS H:160 , LYS H:162 , ASP H:321 , ASP H:323 , GLU H:2485
BINDING SITE FOR RESIDUE ALA H 2484
24
CC6
SOFTWARE
ARG H:24 , ILE H:54 , LYS H:160 , LYS H:162 , ASP H:191 , ASP H:244 , LYS H:268 , SER H:296 , MET H:297 , ILE H:298 , MG H:1608 , ALA H:2484 , HOH H:2493 , HOH H:2550
BINDING SITE FOR RESIDUE GLU H 2485
[
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, 16)
Info
All SCOP Domains
1a: SCOP_d1tkka2 (A:2-125)
1b: SCOP_d1tkkg2 (G:2-125)
1c: SCOP_d1tkkh2 (H:2-125)
1d: SCOP_d1tkkb2 (B:2-125)
1e: SCOP_d1tkkc2 (C:2-125)
1f: SCOP_d1tkkd2 (D:2-125)
1g: SCOP_d1tkke2 (E:2-125)
1h: SCOP_d1tkkf2 (F:2-125)
2a: SCOP_d1tkka1 (A:126-358)
2b: SCOP_d1tkkg1 (G:126-358)
2c: SCOP_d1tkkh1 (H:126-358)
2d: SCOP_d1tkkb1 (B:126-358)
2e: SCOP_d1tkkc1 (C:126-358)
2f: SCOP_d1tkkd1 (D:126-358)
2g: SCOP_d1tkke1 (E:126-358)
2h: SCOP_d1tkkf1 (F:126-358)
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
:
Enolase N-terminal domain-like
(88)
Protein domain
:
L-Ala-D/L-Glu epimerase
(3)
Bacillus subtilis [TaxId: 1423]
(2)
1a
d1tkka2
A:2-125
1b
d1tkkg2
G:2-125
1c
d1tkkh2
H:2-125
1d
d1tkkb2
B:2-125
1e
d1tkkc2
C:2-125
1f
d1tkkd2
D:2-125
1g
d1tkke2
E:2-125
1h
d1tkkf2
F:2-125
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Enolase C-terminal domain-like
(212)
Family
:
D-glucarate dehydratase-like
(65)
Protein domain
:
L-Ala-D/L-Glu epimerase
(3)
Bacillus subtilis [TaxId: 1423]
(2)
2a
d1tkka1
A:126-358
2b
d1tkkg1
G:126-358
2c
d1tkkh1
H:126-358
2d
d1tkkb1
B:126-358
2e
d1tkkc1
C:126-358
2f
d1tkkd1
D:126-358
2g
d1tkke1
E:126-358
2h
d1tkkf1
F:126-358
[
close SCOP info
]
CATH Domains
(2, 16)
Info
all CATH domains
1a: CATH_1tkkA01 (A:1-115)
1b: CATH_1tkkG01 (G:1-115)
1c: CATH_1tkkB01 (B:2-115)
1d: CATH_1tkkC01 (C:2-115)
1e: CATH_1tkkD01 (D:2-115)
1f: CATH_1tkkE01 (E:2-115)
1g: CATH_1tkkF01 (F:2-115)
1h: CATH_1tkkH01 (H:2-115)
2a: CATH_1tkkA02 (A:116-359)
2b: CATH_1tkkC02 (C:116-359)
2c: CATH_1tkkD02 (D:116-359)
2d: CATH_1tkkE02 (E:116-359)
2e: CATH_1tkkG02 (G:116-359)
2f: CATH_1tkkH02 (H:116-359)
2g: CATH_1tkkB02 (B:116-358)
2h: CATH_1tkkF02 (F:116-358)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Enolase-like; domain 1
(252)
Homologous Superfamily
:
Enolase-like, N-terminal domain
(130)
Bacillus subtilis. Organism_taxid: 1423.
(2)
1a
1tkkA01
A:1-115
1b
1tkkG01
G:1-115
1c
1tkkB01
B:2-115
1d
1tkkC01
C:2-115
1e
1tkkD01
D:2-115
1f
1tkkE01
E:2-115
1g
1tkkF01
F:2-115
1h
1tkkH01
H:2-115
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Enolase superfamily
(142)
Bacillus subtilis. Organism_taxid: 1423.
(2)
2a
1tkkA02
A:116-359
2b
1tkkC02
C:116-359
2c
1tkkD02
D:116-359
2d
1tkkE02
E:116-359
2e
1tkkG02
G:116-359
2f
1tkkH02
H:116-359
2g
1tkkB02
B:116-358
2h
1tkkF02
F:116-358
[
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
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 (473 KB)
Header - Asym.Unit
Biol.Unit 1 (466 KB)
Header - Biol.Unit 1
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
1TKK
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help