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.
3A12
Biol. Unit 2
Info
Asym.Unit (739 KB)
Biol.Unit 1 (734 KB)
Biol.Unit 2 (725 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 TYPE III RUBISCO COMPLEXED WITH 2-CABP
Authors
:
Y. Nishitani, M. Fujihashi, T. Doi, S. Yoshida, H. Atomi, T. Imanaka, K.
Date
:
25 Mar 09 (Deposition) - 07 Apr 10 (Release) - 02 Feb 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J
Biol. Unit 1: A,B,C,D,E (2x)
Biol. Unit 2: F,G,H,I,J (2x)
Keywords
:
Ribulose-1, 5-Bisphosphate Carboxylase/Oxygenase, Rubisco, Lyase, Carbon Dioxide Fixation, Magnesium, Metal-Binding, Monooxygenase, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Nishitani, S. Yoshida, M. Fujihashi, K. Kitagawa, T. Doi, H. Atomi, T. Imanaka, K. Miki
Structure-Based Catalytic Optimization Of A Type Iii Rubisc From A Hyperthermophile
J. Biol. Chem. V. 285 39339 2010
[
close entry info
]
Hetero Components
(2, 20)
Info
All Hetero Components
1a: 2-CARBOXYARABINITOL-1,5-DIPHOSPHAT... (CAPa)
1b: 2-CARBOXYARABINITOL-1,5-DIPHOSPHAT... (CAPb)
1c: 2-CARBOXYARABINITOL-1,5-DIPHOSPHAT... (CAPc)
1d: 2-CARBOXYARABINITOL-1,5-DIPHOSPHAT... (CAPd)
1e: 2-CARBOXYARABINITOL-1,5-DIPHOSPHAT... (CAPe)
1f: 2-CARBOXYARABINITOL-1,5-DIPHOSPHAT... (CAPf)
1g: 2-CARBOXYARABINITOL-1,5-DIPHOSPHAT... (CAPg)
1h: 2-CARBOXYARABINITOL-1,5-DIPHOSPHAT... (CAPh)
1i: 2-CARBOXYARABINITOL-1,5-DIPHOSPHAT... (CAPi)
1j: 2-CARBOXYARABINITOL-1,5-DIPHOSPHAT... (CAPj)
2a: LYSINE NZ-CARBOXYLIC ACID (KCXa)
2b: LYSINE NZ-CARBOXYLIC ACID (KCXb)
2c: LYSINE NZ-CARBOXYLIC ACID (KCXc)
2d: LYSINE NZ-CARBOXYLIC ACID (KCXd)
2e: LYSINE NZ-CARBOXYLIC ACID (KCXe)
2f: LYSINE NZ-CARBOXYLIC ACID (KCXf)
2g: LYSINE NZ-CARBOXYLIC ACID (KCXg)
2h: LYSINE NZ-CARBOXYLIC ACID (KCXh)
2i: LYSINE NZ-CARBOXYLIC ACID (KCXi)
2j: LYSINE NZ-CARBOXYLIC ACID (KCXj)
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)
3j: MAGNESIUM ION (MGj)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CAP
10
Ligand/Ion
2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
2
KCX
10
Mod. Amino Acid
LYSINE NZ-CARBOXYLIC ACID
3
MG
-1
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(10, 10)
Info
All Sites
01: BC2 (SOFTWARE)
02: BC3 (SOFTWARE)
03: BC4 (SOFTWARE)
04: BC5 (SOFTWARE)
05: BC6 (SOFTWARE)
06: BC7 (SOFTWARE)
07: BC8 (SOFTWARE)
08: BC9 (SOFTWARE)
09: CC1 (SOFTWARE)
10: CC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
BC2
SOFTWARE
KCX F:189 , ASP F:191 , GLU F:192 , CAP F:446
BINDING SITE FOR RESIDUE MG F 445
02
BC3
SOFTWARE
LYS F:163 , LYS F:165 , KCX F:189 , ASP F:191 , GLU F:192 , HIS F:281 , ARG F:282 , HIS F:314 , LYS F:322 , LEU F:323 , SER F:367 , GLY F:368 , GLY F:369 , GLN F:389 , GLY F:391 , GLY F:392 , MG F:445 , HOH F:519 , HOH F:525 , HOH F:536 , HOH F:537 , HOH F:556 , GLU H:49 , THR H:54 , TRP H:55 , ASN H:111 , HOH H:513
BINDING SITE FOR RESIDUE CAP F 446
03
BC4
SOFTWARE
KCX G:189 , ASP G:191 , GLU G:192 , CAP G:446
BINDING SITE FOR RESIDUE MG G 445
04
BC5
SOFTWARE
GLU G:49 , TRP G:55 , ASN G:111 , LYS G:163 , LYS G:165 , KCX G:189 , ASP G:191 , GLU G:192 , HIS G:281 , ARG G:282 , HIS G:314 , LYS G:322 , LEU G:323 , SER G:367 , GLY G:368 , GLY G:369 , GLN G:389 , GLY G:391 , GLY G:392 , MG G:445 , HOH G:507 , HOH G:524 , HOH G:529 , HOH G:536 , HOH G:540 , HOH G:561 , HOH G:574 , HOH G:602 , HOH G:607
BINDING SITE FOR RESIDUE CAP G 446
05
BC6
SOFTWARE
ASN F:111 , LYS H:163 , LYS H:165 , KCX H:189 , ASP H:191 , GLU H:192 , CAP H:446
BINDING SITE FOR RESIDUE MG H 445
06
BC7
SOFTWARE
GLU F:49 , TRP F:55 , ASN F:111 , LYS H:163 , LYS H:165 , KCX H:189 , ASP H:191 , GLU H:192 , HIS H:281 , ARG H:282 , HIS H:314 , LYS H:322 , LEU H:323 , SER H:367 , GLY H:368 , GLY H:369 , GLN H:389 , GLY H:391 , GLY H:392 , MG H:445 , HOH H:520 , HOH H:547 , HOH H:571 , HOH H:584 , HOH H:595 , HOH H:601 , HOH H:604 , HOH H:613
BINDING SITE FOR RESIDUE CAP H 446
07
BC8
SOFTWARE
KCX I:189 , ASP I:191 , GLU I:192 , CAP I:446
BINDING SITE FOR RESIDUE MG I 445
08
BC9
SOFTWARE
LYS I:163 , LYS I:165 , KCX I:189 , ASP I:191 , GLU I:192 , HIS I:281 , ARG I:282 , HIS I:314 , LYS I:322 , LEU I:323 , SER I:367 , GLY I:368 , GLY I:369 , GLN I:389 , GLY I:391 , GLY I:392 , MG I:445 , HOH I:515 , HOH I:518 , HOH I:521 , HOH I:525 , HOH I:531 , HOH I:616 , HOH I:662 , HOH I:744 , GLU J:49 , TRP J:55 , ASN J:111
BINDING SITE FOR RESIDUE CAP I 446
09
CC1
SOFTWARE
ASN I:111 , LYS J:163 , KCX J:189 , ASP J:191 , GLU J:192 , CAP J:446
BINDING SITE FOR RESIDUE MG J 445
10
CC2
SOFTWARE
GLU I:49 , TRP I:55 , ASN I:111 , HOH I:603 , LYS J:163 , LYS J:165 , KCX J:189 , ASP J:191 , GLU J:192 , HIS J:281 , ARG J:282 , HIS J:314 , LYS J:322 , LEU J:323 , SER J:367 , GLY J:368 , GLY J:369 , GLN J:389 , GLY J:391 , GLY J:392 , MG J:445 , HOH J:502 , HOH J:546 , HOH J:566 , HOH J:580 , HOH J:586 , HOH J:587 , HOH J:633
BINDING SITE FOR RESIDUE CAP J 446
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(, 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.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 20)
Info
All SCOP Domains
1a: SCOP_d3a12a1 (A:8-136)
1b: SCOP_d3a12b1 (B:7-136)
1c: SCOP_d3a12c1 (C:7-136)
1d: SCOP_d3a12d1 (D:9-136)
1e: SCOP_d3a12e1 (E:7-136)
1f: SCOP_d3a12f1 (F:9-136)
1g: SCOP_d3a12g1 (G:9-136)
1h: SCOP_d3a12h1 (H:8-136)
1i: SCOP_d3a12i1 (I:9-136)
1j: SCOP_d3a12j1 (J:8-136)
2a: SCOP_d3a12a2 (A:137-444)
2b: SCOP_d3a12b2 (B:137-444)
2c: SCOP_d3a12c2 (C:137-444)
2d: SCOP_d3a12d2 (D:137-444)
2e: SCOP_d3a12e2 (E:137-444)
2f: SCOP_d3a12f2 (F:137-444)
2g: SCOP_d3a12g2 (G:137-444)
2h: SCOP_d3a12h2 (H:137-444)
2i: SCOP_d3a12i2 (I:137-444)
2j: SCOP_d3a12j2 (J:137-444)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Ferredoxin-like
(1795)
Superfamily
:
RuBisCO, large subunit, small (N-terminal) domain
(66)
Family
:
Ribulose 1,5-bisphosphate carboxylase-oxygenase
(39)
Protein domain
:
Ribulose 1,5-bisphosphate carboxylase-oxygenase
(39)
Thermococcus kodakaraensis [TaxId: 311400]
(2)
1a
d3a12a1
A:8-136
1b
d3a12b1
B:7-136
1c
d3a12c1
C:7-136
1d
d3a12d1
D:9-136
1e
d3a12e1
E:7-136
1f
d3a12f1
F:9-136
1g
d3a12g1
G:9-136
1h
d3a12h1
H:8-136
1i
d3a12i1
I:9-136
1j
d3a12j1
J:8-136
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
RuBisCo, C-terminal domain
(66)
Family
:
RuBisCo, large subunit, C-terminal domain
(56)
Protein domain
:
Ribulose 1,5-bisphosphate carboxylase-oxygenase
(40)
Thermococcus kodakaraensis [TaxId: 311400]
(2)
2a
d3a12a2
A:137-444
2b
d3a12b2
B:137-444
2c
d3a12c2
C:137-444
2d
d3a12d2
D:137-444
2e
d3a12e2
E:137-444
2f
d3a12f2
F:137-444
2g
d3a12g2
G:137-444
2h
d3a12h2
H:137-444
2i
d3a12i2
I:137-444
2j
d3a12j2
J:137-444
[
close SCOP info
]
CATH Domains
(2, 20)
Info
all CATH domains
1a: CATH_3a12F01 (F:9-136)
1b: CATH_3a12D01 (D:9-136)
1c: CATH_3a12E01 (E:7-136)
1d: CATH_3a12G01 (G:9-136)
1e: CATH_3a12I01 (I:9-136)
1f: CATH_3a12A01 (A:8-136)
1g: CATH_3a12H01 (H:8-136)
1h: CATH_3a12J01 (J:8-136)
1i: CATH_3a12B01 (B:7-136)
1j: CATH_3a12C01 (C:7-136)
2a: CATH_3a12A02 (A:137-438)
2b: CATH_3a12B02 (B:137-438)
2c: CATH_3a12C02 (C:137-438)
2d: CATH_3a12D02 (D:137-438)
2e: CATH_3a12F02 (F:137-438)
2f: CATH_3a12G02 (G:137-438)
2g: CATH_3a12H02 (H:137-438)
2h: CATH_3a12I02 (I:137-438)
2i: CATH_3a12J02 (J:137-438)
2j: CATH_3a12E02 (E:137-438)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Alpha-Beta Plaits
(1688)
Homologous Superfamily
:
[code=3.30.70.150, no name defined]
(49)
Thermococcus kodakaraensis (Pyrococcus kodakaraensis)
(2)
1a
3a12F01
F:9-136
1b
3a12D01
D:9-136
1c
3a12E01
E:7-136
1d
3a12G01
G:9-136
1e
3a12I01
I:9-136
1f
3a12A01
A:8-136
1g
3a12H01
H:8-136
1h
3a12J01
J:8-136
1i
3a12B01
B:7-136
1j
3a12C01
C:7-136
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Rubisco
(49)
Thermococcus kodakaraensis (Pyrococcus kodakaraensis)
(2)
2a
3a12A02
A:137-438
2b
3a12B02
B:137-438
2c
3a12C02
C:137-438
2d
3a12D02
D:137-438
2e
3a12F02
F:137-438
2f
3a12G02
G:137-438
2g
3a12H02
H:137-438
2h
3a12I02
I:137-438
2i
3a12J02
J:137-438
2j
3a12E02
E:137-438
[
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 F
Chain G
Chain H
Chain I
Chain J
Asymmetric Unit 1
Asymmetric Unit 2
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 (739 KB)
Header - Asym.Unit
Biol.Unit 1 (734 KB)
Header - Biol.Unit 1
Biol.Unit 2 (725 KB)
Header - Biol.Unit 2
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
3A12
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help