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.
1I9C
Asym. Unit
Info
Asym.Unit (236 KB)
Biol.Unit 1 (229 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
GLUTAMATE MUTASE FROM CLOSTRIDIUM COCHLEARIUM: COMPLEX WITH ADENOSYLCOBALAMIN AND SUBSTRATE
Authors
:
K. Gruber, C. Kratky
Date
:
19 Mar 01 (Deposition) - 19 Mar 02 (Release) - 24 Oct 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Coenzyme B12, Radical Reaction, Ribose Pseudorotation, Tim-Barrel, Rossman-Fold, Isomerase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Gruber, R. Reitzer, C. Kratky
Radical Shuttling In A Protein: Ribose Pseudorotation Controls Alkyl-Radical Transfer In The Coenzyme B(12) Dependent Enzyme Glutamate Mutase
Angew. Chem. Int. Ed. Engl. V. 40 3377 2001
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(4, 8)
Info
All Hetero Components
1a: (2S,3S)-3-METHYL-ASPARTIC ACID (2ASa)
1b: (2S,3S)-3-METHYL-ASPARTIC ACID (2ASb)
2a: 5'-DEOXYADENOSINE (5ADa)
2b: 5'-DEOXYADENOSINE (5ADb)
3a: COBALAMIN (B12a)
3b: COBALAMIN (B12b)
4a: GLUTAMIC ACID (GLUa)
4b: GLUTAMIC ACID (GLUb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
2AS
2
Ligand/Ion
(2S,3S)-3-METHYL-ASPARTIC ACID
2
5AD
2
Ligand/Ion
5'-DEOXYADENOSINE
3
B12
2
Ligand/Ion
COBALAMIN
4
GLU
2
Mod. Amino Acid
GLUTAMIC ACID
[
close Hetero Component info
]
Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
SER A:13 , ASP A:14 , CYS A:15 , HIS A:16 , ALA A:17 , VAL A:18 , GLY A:19 , ILE A:22 , LEU A:23 , SER A:61 , LEU A:63 , TYR A:64 , GLY A:65 , GLY A:91 , GLY A:92 , ASN A:93 , VAL A:95 , VAL A:96 , GLY A:97 , THR A:121 , HOH A:804 , HOH A:806 , HOH A:807 , HOH A:809 , HOH A:814 , HOH A:816 , HOH A:855 , ILE B:95 , ALA B:97 , ARG B:100 , ASN B:123 , PRO B:180 , LEU B:219 , THR B:220 , MET B:294 , GLY B:295 , GLY B:296 , PHE B:297 , HIS B:329 , GLU B:330 , GLY B:333 , ILE B:334 , PHE B:471 , 5AD B:1303 , GLU B:1305 , HOH B:1363
BINDING SITE FOR RESIDUE B12 A 800
2
AC2
SOFTWARE
SER C:13 , ASP C:14 , CYS C:15 , HIS C:16 , ALA C:17 , VAL C:18 , GLY C:19 , LEU C:23 , SER C:61 , LEU C:63 , TYR C:64 , GLY C:65 , GLY C:91 , GLY C:92 , ASN C:93 , VAL C:95 , VAL C:96 , GLY C:97 , THR C:121 , PRO C:123 , HOH C:801 , HOH C:805 , HOH C:808 , HOH C:809 , HOH C:813 , HOH C:817 , HOH C:833 , ILE D:95 , ALA D:97 , ARG D:100 , ASN D:123 , PRO D:180 , THR D:220 , MET D:294 , GLY D:295 , GLY D:296 , PHE D:297 , HIS D:329 , GLU D:330 , ALA D:331 , GLY D:333 , ILE D:334 , PRO D:410 , PHE D:471 , 5AD D:1304 , GLU D:1306 , 2AS D:1308 , HOH D:1361
BINDING SITE FOR RESIDUE B12 C 800
3
AC3
SOFTWARE
B12 A:800 , ARG B:66 , ALA B:67 , GLY B:68 , THR B:94 , ASN B:123 , LYS B:326 , GLU B:330 , ILE B:334 , PRO B:335 , GLU B:1305 , 2AS B:1307 , HOH B:1330 , HOH B:1335 , HOH B:1378 , HOH B:1436
BINDING SITE FOR RESIDUE 5AD B 1303
4
AC4
SOFTWARE
B12 C:800 , ARG D:66 , ALA D:67 , GLY D:68 , THR D:94 , ASN D:123 , LYS D:326 , GLU D:330 , ILE D:334 , PRO D:335 , GLU D:1306 , 2AS D:1308 , HOH D:1314 , HOH D:1322 , HOH D:1380 , HOH D:1454
BINDING SITE FOR RESIDUE 5AD D 1304
5
AC5
SOFTWARE
B12 A:800 , ARG B:66 , THR B:94 , ARG B:100 , ARG B:149 , HIS B:150 , GLU B:171 , TYR B:177 , TYR B:181 , PHE B:216 , HIS B:291 , 5AD B:1303 , HOH B:1315
BINDING SITE FOR RESIDUE GLU B 1305
6
AC6
SOFTWARE
ARG B:66 , THR B:94 , ARG B:100 , ARG B:149 , HIS B:150 , GLU B:171 , TYR B:177 , TYR B:181 , PHE B:216 , HIS B:291 , 5AD B:1303 , HOH B:1315
BINDING SITE FOR RESIDUE 2AS B 1307
7
AC7
SOFTWARE
B12 C:800 , ARG D:66 , THR D:94 , ARG D:100 , ARG D:149 , HIS D:150 , GLU D:171 , TYR D:177 , TYR D:181 , PHE D:216 , HIS D:291 , 5AD D:1304 , HOH D:1325
BINDING SITE FOR RESIDUE GLU D 1306
8
AC8
SOFTWARE
B12 C:800 , ARG D:66 , ARG D:100 , ARG D:149 , HIS D:150 , GLU D:171 , TYR D:177 , TYR D:181 , PHE D:216 , HIS D:291 , 5AD D:1304 , HOH D:1325
BINDING SITE FOR RESIDUE 2AS D 1308
[
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, 2)
Info
All PROSITE Patterns/Profiles
1: B12_BINDING (A:3-137,C:3-137)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
B12_BINDING
PS51332
B12-binding domain profile.
GMSS_CLOCO
3-137
2
A:3-137
C:3-137
[
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, 4)
Info
All SCOP Domains
1a: SCOP_d1i9ca_ (A:)
1b: SCOP_d1i9cc_ (C:)
2a: SCOP_d1i9cb_ (B:)
2b: SCOP_d1i9cd_ (D:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Flavodoxin-like
(1057)
Superfamily
:
Cobalamin (vitamin B12)-binding domain
(29)
Family
:
Cobalamin (vitamin B12)-binding domain
(29)
Protein domain
:
Glutamate mutase, small subunit
(7)
Clostridium cochlearium [TaxId: 1494]
(4)
1a
d1i9ca_
A:
1b
d1i9cc_
C:
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
Cobalamin (vitamin B12)-dependent enzymes
(30)
Family
:
Glutamate mutase, large subunit
(3)
Protein domain
:
Glutamate mutase, large subunit
(3)
Clostridium cochlearium [TaxId: 1494]
(3)
2a
d1i9cb_
B:
2b
d1i9cd_
D:
[
close SCOP info
]
CATH Domains
(3, 6)
Info
all CATH domains
1a: CATH_1i9cA00 (A:1-137)
1b: CATH_1i9cC00 (C:1-137)
2a: CATH_1i9cB01 (B:1-417)
2b: CATH_1i9cD01 (D:1-417)
3a: CATH_1i9cB02 (B:418-483)
3b: CATH_1i9cD02 (D:418-483)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.280, no name defined]
(23)
Clostridium cochlearium. Organism_taxid: 1494.
(4)
1a
1i9cA00
A:1-137
1b
1i9cC00
C:1-137
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
[code=3.20.20.240, no name defined]
(12)
Clostridium cochlearium. Organism_taxid: 1494.
(3)
2a
1i9cB01
B:1-417
2b
1i9cD01
D:1-417
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Glutamate mutase, C-terminal domain
(3)
Homologous Superfamily
:
[code=3.90.970.10, no name defined]
(3)
Clostridium cochlearium. Organism_taxid: 1494.
(3)
3a
1i9cB02
B:418-483
3b
1i9cD02
D:418-483
[
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 (236 KB)
Header - Asym.Unit
Biol.Unit 1 (229 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
1I9C
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help