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.
3RUP
Asym. Unit
Info
Asym.Unit (165 KB)
Biol.Unit 1 (158 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 E.COLI BIOTIN CARBOXYLASE IN COMPLEX WITH TWO ADP AND TWO CA IONS
Authors
:
C. Y. Chou, L. Tong
Date
:
05 May 11 (Deposition) - 18 May 11 (Release) - 20 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.99
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Ligase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. Y. Chou, L. Tong
Structural And Biochemical Studies On The Regulation Of Biotin Carboxylase By Substrate Inhibition And Dimerization
J. Biol. Chem. V. 286 24417 2011
[
close entry info
]
Hetero Components
(3, 11)
Info
All Hetero Components
1a: ADENOSINE-5'-DIPHOSPHATE (ADPa)
1b: ADENOSINE-5'-DIPHOSPHATE (ADPb)
1c: ADENOSINE-5'-DIPHOSPHATE (ADPc)
1d: ADENOSINE-5'-DIPHOSPHATE (ADPd)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
2d: CALCIUM ION (CAd)
3a: CHLORIDE ION (CLa)
3b: CHLORIDE ION (CLb)
3c: CHLORIDE ION (CLc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ADP
4
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
2
CA
4
Ligand/Ion
CALCIUM ION
3
CL
3
Ligand/Ion
CHLORIDE ION
[
close Hetero Component info
]
Sites
(11, 11)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY A:83 , GLU A:87 , GLY A:162 , GLY A:164 , GLY A:165 , ARG A:167 , PHE A:193 , GLN A:237 , LYS A:238 , ASN A:290 , ARG A:292 , GLN A:294 , VAL A:295 , GLU A:296 , ARG A:338 , ASP A:382 , HOH A:459 , HOH A:505 , HOH A:510 , HOH A:531 , HOH A:594 , HOH A:607 , HOH A:619
BINDING SITE FOR RESIDUE ADP A 1000
02
AC2
SOFTWARE
LYS A:116 , LYS A:159 , GLY A:163 , GLY A:164 , GLY A:165 , GLY A:166 , MET A:169 , GLU A:201 , LYS A:202 , TYR A:203 , LEU A:204 , HIS A:209 , GLN A:233 , HIS A:236 , GLU A:276 , LEU A:278 , GLU A:288 , ILE A:437 , HOH A:459 , HOH A:518 , HOH A:530 , HOH A:553 , CA A:1004
BINDING SITE FOR RESIDUE ADP A 1002
03
AC3
SOFTWARE
GLU A:276 , GLU A:288 , HOH A:530 , HOH A:619 , ADP A:1002
BINDING SITE FOR RESIDUE CA A 1004
04
AC4
SOFTWARE
GLU A:87 , GLU A:288 , ASN A:290 , HOH A:486 , HOH A:531 , HOH A:538
BINDING SITE FOR RESIDUE CA A 1006
05
AC5
SOFTWARE
ARG A:10 , HIS A:370 , TYR A:375 , PRO A:378 , HOH A:863
BINDING SITE FOR RESIDUE CL A 1008
06
AC6
SOFTWARE
LYS B:116 , LYS B:159 , GLY B:163 , GLY B:164 , GLY B:165 , GLY B:166 , MET B:169 , GLU B:201 , LYS B:202 , TYR B:203 , LEU B:204 , HIS B:209 , GLN B:233 , HIS B:236 , GLU B:276 , LEU B:278 , ILE B:287 , GLU B:288 , ILE B:437 , HOH B:536 , HOH B:545 , HOH B:609 , HOH B:623 , CA B:1005
BINDING SITE FOR RESIDUE ADP B 1001
07
AC7
SOFTWARE
GLY B:83 , GLU B:87 , GLY B:162 , GLY B:164 , GLY B:165 , GLN B:237 , LYS B:238 , ASN B:290 , ARG B:292 , GLN B:294 , VAL B:295 , GLU B:296 , ARG B:338 , ASP B:382 , HOH B:492 , HOH B:536 , HOH B:538 , HOH B:540 , HOH B:544 , HOH B:617 , HOH B:623 , HOH B:808
BINDING SITE FOR RESIDUE ADP B 1003
08
AC8
SOFTWARE
GLU B:276 , GLU B:288 , HOH B:545 , HOH B:623 , ADP B:1001
BINDING SITE FOR RESIDUE CA B 1005
09
AC9
SOFTWARE
GLU B:87 , GLU B:288 , ASN B:290 , HOH B:492 , HOH B:540 , HOH B:622
BINDING SITE FOR RESIDUE CA B 1007
10
BC1
SOFTWARE
ARG B:10 , HIS B:370 , TYR B:375
BINDING SITE FOR RESIDUE CL B 1009
11
BC2
SOFTWARE
GLY B:11 , HIS B:41 , HIS B:370
BINDING SITE FOR RESIDUE CL B 1011
[
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
(3, 6)
Info
All PROSITE Patterns/Profiles
1: BC (A:1-444,B:1-445)
2: CPSASE_1 (A:154-168,B:154-168)
3: CPSASE_2 (A:286-293,B:286-293)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
BC
PS50979
Biotin carboxylation domain profile.
ACCC_ECOLI
1-445
2
A:1-444
B:1-445
2
CPSASE_1
PS00866
Carbamoyl-phosphate synthase subdomain signature 1.
ACCC_ECOLI
154-168
2
A:154-168
B:154-168
3
CPSASE_2
PS00867
Carbamoyl-phosphate synthase subdomain signature 2.
ACCC_ECOLI
286-293
2
A:286-293
B:286-293
[
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
(3, 6)
Info
All SCOP Domains
1a: SCOP_d3rupa3 (A:331-444)
1b: SCOP_d3rupb3 (B:331-446)
2a: SCOP_d3rupa2 (A:115-330)
2b: SCOP_d3rupb2 (B:115-330)
3a: SCOP_d3rupa1 (A:1-114)
3b: SCOP_d3rupb1 (B:1-114)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Barrel-sandwich hybrid
(185)
Superfamily
:
Rudiment single hybrid motif
(69)
Family
:
BC C-terminal domain-like
(40)
Protein domain
:
Biotin carboxylase (BC), C-domain
(25)
Escherichia coli [TaxId: 562]
(24)
1a
d3rupa3
A:331-444
1b
d3rupb3
B:331-446
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
ATP-grasp
(191)
Superfamily
:
Glutathione synthetase ATP-binding domain-like
(158)
Family
:
BC ATP-binding domain-like
(53)
Protein domain
:
Biotin carboxylase (BC), domain 2
(25)
Escherichia coli [TaxId: 562]
(24)
2a
d3rupa2
A:115-330
2b
d3rupb2
B:115-330
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
PreATP-grasp domain
(131)
Superfamily
:
PreATP-grasp domain
(131)
Family
:
BC N-terminal domain-like
(50)
Protein domain
:
Biotin carboxylase (BC), N-terminal domain
(25)
Escherichia coli [TaxId: 562]
(24)
3a
d3rupa1
A:1-114
3b
d3rupb1
B:1-114
[
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
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 (165 KB)
Header - Asym.Unit
Biol.Unit 1 (158 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
3RUP
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
