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.
1IGW
Asym. Unit
Info
Asym.Unit (280 KB)
Biol.Unit 1 (272 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 THE ISOCITRATE LYASE FROM THE A219C MUTANT OF ESCHERICHIA COLI
Authors
:
K. L. Britton, I. S. B. Abeysinghe, P. J. Baker, V. Barynin, P. Diehl, S. J. Langridge, B. A. Mcfadden, S. E. Sedelnikova, T. J. Stillman, K. Weeradechapon, D. W. Rice
Date
:
18 Apr 01 (Deposition) - 05 Sep 01 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Beta Barrel, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. L. Britton, I. S. Abeysinghe, P. J. Baker, V. Barynin, P. Diehl, S. J. Langridge, B. A. Mcfadden, S. E. Sedelnikova, T. J. Stillman, K. Weeradechapon, D. W. Rice
The Structure And Domain Organization Of Escherichia Coli Isocitrate Lyase.
Acta Crystallogr. , Sect. D V. 57 1209 2001
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 29)
Info
All Hetero Components
1a: MERCURY (II) ION (HGa)
1b: MERCURY (II) ION (HGb)
1c: MERCURY (II) ION (HGc)
1d: MERCURY (II) ION (HGd)
1e: MERCURY (II) ION (HGe)
1f: MERCURY (II) ION (HGf)
1g: MERCURY (II) ION (HGg)
1h: MERCURY (II) ION (HGh)
1i: MERCURY (II) ION (HGi)
1j: MERCURY (II) ION (HGj)
1k: MERCURY (II) ION (HGk)
1l: MERCURY (II) ION (HGl)
1m: MERCURY (II) ION (HGm)
1n: MERCURY (II) ION (HGn)
1o: MERCURY (II) ION (HGo)
1p: MERCURY (II) ION (HGp)
1q: MERCURY (II) ION (HGq)
1r: MERCURY (II) ION (HGr)
1s: MERCURY (II) ION (HGs)
1t: MERCURY (II) ION (HGt)
1u: MERCURY (II) ION (HGu)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
3a: PYRUVIC ACID (PYRa)
3b: PYRUVIC ACID (PYRb)
3c: PYRUVIC ACID (PYRc)
3d: PYRUVIC ACID (PYRd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
HG
21
Ligand/Ion
MERCURY (II) ION
2
MG
4
Ligand/Ion
MAGNESIUM ION
3
PYR
4
Ligand/Ion
PYRUVIC ACID
[
close Hetero Component info
]
Sites
(29, 29)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:42 , CYS A:43 , HOH A:1445 , HOH A:1600
BINDING SITE FOR RESIDUE HG A 435
02
AC2
SOFTWARE
LYS A:173 , CYS A:219 , THR A:223 , HOH C:1514 , HOH C:1571
BINDING SITE FOR RESIDUE HG A 436
03
AC3
SOFTWARE
CYS A:245 , ASP A:246 , HOH B:1609
BINDING SITE FOR RESIDUE HG A 437
04
AC4
SOFTWARE
CYS A:288 , THR A:290 , HOH A:1561
BINDING SITE FOR RESIDUE HG A 438
05
AC5
SOFTWARE
CYS A:318 , HOH A:1461 , HOH A:1507 , HOH A:1549 , MET D:375
BINDING SITE FOR RESIDUE HG A 439
06
AC6
SOFTWARE
GLU B:42 , CYS B:43 , HOH B:1509
BINDING SITE FOR RESIDUE HG B 435
07
AC7
SOFTWARE
CYS B:219 , THR B:223
BINDING SITE FOR RESIDUE HG B 436
08
AC8
SOFTWARE
CYS B:245
BINDING SITE FOR RESIDUE HG B 437
09
AC9
SOFTWARE
CYS B:288 , THR B:290 , HOH B:1570
BINDING SITE FOR RESIDUE HG B 438
10
BC1
SOFTWARE
CYS B:318 , PHE B:349 , HOH B:1512 , MET C:375
BINDING SITE FOR RESIDUE HG B 439
11
BC2
SOFTWARE
GLU C:42 , CYS C:43
BINDING SITE FOR RESIDUE HG C 435
12
BC3
SOFTWARE
HOH A:1596 , CYS C:219 , THR C:223
BINDING SITE FOR RESIDUE HG C 436
13
BC4
SOFTWARE
CYS C:245 , ASP C:246 , HOH C:1652 , GLU D:260
BINDING SITE FOR RESIDUE HG C 437
14
BC5
SOFTWARE
CYS C:288 , THR C:290 , HOH C:1516 , HOH C:1640
BINDING SITE FOR RESIDUE HG C 438
15
BC6
SOFTWARE
MET B:375 , CYS C:318 , PHE C:349 , HOH C:1510 , HOH C:1561
BINDING SITE FOR RESIDUE HG C 439
16
BC7
SOFTWARE
CYS C:195 , HIS C:197
BINDING SITE FOR RESIDUE HG C 440
17
BC8
SOFTWARE
GLU D:42 , CYS D:43
BINDING SITE FOR RESIDUE HG D 435
18
BC9
SOFTWARE
LYS D:173 , CYS D:219 , THR D:223
BINDING SITE FOR RESIDUE HG D 436
19
CC1
SOFTWARE
GLU C:260 , HOH C:1688 , CYS D:245 , ASP D:246
BINDING SITE FOR RESIDUE HG D 437
20
CC2
SOFTWARE
CYS D:288 , THR D:290
BINDING SITE FOR RESIDUE HG D 438
21
CC3
SOFTWARE
CYS D:318 , GLN D:337 , PHE D:349 , HOH D:1562
BINDING SITE FOR RESIDUE HG D 439
22
CC4
SOFTWARE
ASP A:157 , PYR A:1444 , HOH A:1630 , HOH A:1631 , HOH A:1632
BINDING SITE FOR RESIDUE MG A 441
23
CC5
SOFTWARE
ASP B:157 , PYR B:1445 , HOH B:1633 , HOH B:1634 , HOH B:1635
BINDING SITE FOR RESIDUE MG B 441
24
CC6
SOFTWARE
ASP C:157 , PYR C:1446 , HOH C:1694 , HOH C:1695 , HOH C:1696
BINDING SITE FOR RESIDUE MG C 441
25
CC7
SOFTWARE
ASP D:157 , PYR D:1447 , HOH D:1584 , HOH D:1585 , HOH D:1586
BINDING SITE FOR RESIDUE MG D 441
26
CC8
SOFTWARE
TYR A:89 , SER A:91 , GLY A:92 , TRP A:93 , ASP A:157 , HIS A:184 , ARG A:232 , THR A:351 , MG A:441 , HOH A:1570 , HOH A:1630 , HOH A:1631 , HOH A:1632
BINDING SITE FOR RESIDUE PYR A 1444
27
CC9
SOFTWARE
TYR B:89 , SER B:91 , GLY B:92 , TRP B:93 , ASP B:157 , HIS B:184 , ARG B:232 , THR B:351 , MG B:441 , HOH B:1633 , HOH B:1635
BINDING SITE FOR RESIDUE PYR B 1445
28
DC1
SOFTWARE
TYR C:89 , SER C:91 , GLY C:92 , TRP C:93 , ASP C:157 , HIS C:184 , ARG C:232 , THR C:351 , MG C:441 , HOH C:1552 , HOH C:1635 , HOH C:1695 , HOH C:1696
BINDING SITE FOR RESIDUE PYR C 1446
29
DC2
SOFTWARE
TYR D:89 , SER D:91 , GLY D:92 , TRP D:93 , ASP D:157 , HIS D:184 , ARG D:232 , THR D:351 , MG D:441 , HOH D:1552 , HOH D:1584 , HOH D:1585 , HOH D:1586
BINDING SITE FOR RESIDUE PYR D 1447
[
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
(1, 3)
Info
All PROSITE Patterns/Profiles
1: ISOCITRATE_LYASE (A:193-195,B:193-194,C:193-198)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ISOCITRATE_LYASE
PS00161
Isocitrate lyase signature.
ACEA_ECOLI
193-198
3
A:193-195
B:193-194
C:193-198
[
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
(1, 4)
Info
All SCOP Domains
1a: SCOP_d1igwa_ (A:)
1b: SCOP_d1igwb_ (B:)
1c: SCOP_d1igwc_ (C:)
1d: SCOP_d1igwd_ (D:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Phosphoenolpyruvate/pyruvate domain
(92)
Family
:
Phosphoenolpyruvate mutase/Isocitrate lyase-like
(20)
Protein domain
:
Isocitrate lyase
(5)
Escherichia coli [TaxId: 562]
(1)
1a
d1igwa_
A:
1b
d1igwb_
B:
1c
d1igwc_
C:
1d
d1igwd_
D:
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1igwA00 (A:2-417)
1b: CATH_1igwD00 (D:2-417)
1c: CATH_1igwB00 (B:2-417)
1d: CATH_1igwC00 (C:2-417)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Phosphoenolpyruvate-binding domains
(67)
Escherichia coli. Organism_taxid: 562.
(5)
1a
1igwA00
A:2-417
1b
1igwD00
D:2-417
1c
1igwB00
B:2-417
1d
1igwC00
C:2-417
[
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
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 (280 KB)
Header - Asym.Unit
Biol.Unit 1 (272 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
1IGW
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help