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.
3KDO
Asym. Unit
Info
Asym.Unit (722 KB)
Biol.Unit 1 (711 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 SP6 MUTANT COMPLEXED WITH 2-CABP
Authors
:
Y. Nishitani, M. Fujihashi, T. Doi, S. Yoshida, H. Atomi, T. Imanaka, K.
Date
:
23 Oct 09 (Deposition) - 06 Oct 10 (Release) - 02 Feb 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.36
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J (1x)
Keywords
:
Ribulose-1, 5-Bisphosphate Carboxylase/Oxygenase, Rubisco, Carbon Dioxide Fixation, Lyase, Magnesium, Metal-Binding, Monooxygenase
(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
(3, 30)
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
10
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(20, 20)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LYS A:163 , LYS A:165 , KCX A:189 , ASP A:191 , GLU A:192 , HIS A:281 , ARG A:282 , HIS A:314 , LYS A:322 , LEU A:323 , SER A:367 , GLY A:368 , GLY A:369 , GLN A:389 , GLY A:391 , GLY A:392 , MG A:500 , HOH A:753 , HOH A:1643 , THR H:54 , TRP H:55 , ASN H:111 , HOH H:1724
BINDING SITE FOR RESIDUE CAP A 600
02
AC2
SOFTWARE
LYS A:165 , KCX A:189 , ASP A:191 , GLU A:192 , CAP A:600 , ASN H:111
BINDING SITE FOR RESIDUE MG A 500
03
AC3
SOFTWARE
LYS B:163 , LYS B:165 , KCX B:189 , ASP B:191 , GLU B:192 , HIS B:281 , ARG B:282 , HIS B:314 , LYS B:322 , LEU B:323 , SER B:367 , GLY B:368 , GLY B:369 , GLN B:389 , GLY B:391 , GLY B:392 , HOH B:445 , HOH B:482 , MG B:500 , HOH B:619 , HOH B:1206 , HOH B:1246 , HOH B:1922 , TRP G:55 , ASN G:111 , HOH G:474 , HOH G:1621
BINDING SITE FOR RESIDUE CAP B 600
04
AC4
SOFTWARE
LYS B:163 , KCX B:189 , ASP B:191 , GLU B:192 , CAP B:600
BINDING SITE FOR RESIDUE MG B 500
05
AC5
SOFTWARE
LYS C:163 , LYS C:165 , KCX C:189 , ASP C:191 , GLU C:192 , HIS C:281 , ARG C:282 , HIS C:314 , LYS C:322 , LEU C:323 , SER C:367 , GLY C:368 , GLY C:369 , GLN C:389 , GLY C:391 , GLY C:392 , HOH C:481 , HOH C:489 , HOH C:497 , MG C:500 , HOH C:1211 , HOH C:1336 , HOH C:1660 , GLU F:49 , TRP F:55 , ASN F:111 , HOH F:452
BINDING SITE FOR RESIDUE CAP C 600
06
AC6
SOFTWARE
KCX C:189 , ASP C:191 , GLU C:192 , CAP C:600
BINDING SITE FOR RESIDUE MG C 500
07
AC7
SOFTWARE
LYS D:163 , LYS D:165 , KCX D:189 , ASP D:191 , GLU D:192 , HIS D:281 , ARG D:282 , HIS D:314 , LYS D:322 , LEU D:323 , SER D:367 , GLY D:368 , GLY D:369 , GLN D:389 , GLY D:391 , GLY D:392 , HOH D:445 , HOH D:465 , HOH D:475 , HOH D:498 , MG D:500 , HOH D:509 , HOH D:992 , HOH D:1580 , GLU J:49 , THR J:54 , TRP J:55 , ASN J:111
BINDING SITE FOR RESIDUE CAP D 600
08
AC8
SOFTWARE
LYS D:165 , KCX D:189 , ASP D:191 , GLU D:192 , CAP D:600
BINDING SITE FOR RESIDUE MG D 500
09
AC9
SOFTWARE
LYS E:163 , LYS E:165 , KCX E:189 , ASP E:191 , GLU E:192 , HIS E:281 , ARG E:282 , HIS E:314 , LYS E:322 , LEU E:323 , SER E:367 , GLY E:368 , GLY E:369 , GLN E:389 , GLY E:391 , GLY E:392 , HOH E:452 , MG E:500 , HOH E:532 , HOH E:956 , HOH E:1175 , HOH E:1679 , TRP I:55 , ASN I:111
BINDING SITE FOR RESIDUE CAP E 600
10
BC1
SOFTWARE
KCX E:189 , ASP E:191 , GLU E:192 , CAP E:600
BINDING SITE FOR RESIDUE MG E 500
11
BC2
SOFTWARE
GLU C:49 , THR C:54 , TRP C:55 , ASN C:111 , HOH C:488 , HOH C:1632 , 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 , HOH F:447 , HOH F:460 , HOH F:485 , MG F:500 , HOH F:1635 , HOH F:1780
BINDING SITE FOR RESIDUE CAP F 600
12
BC3
SOFTWARE
LYS F:165 , KCX F:189 , ASP F:191 , GLU F:192 , CAP F:600
BINDING SITE FOR RESIDUE MG F 500
13
BC4
SOFTWARE
GLU B:49 , TRP B:55 , ASN B:111 , HOH B:452 , HOH B:453 , 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 , HOH G:445 , HOH G:447 , HOH G:454 , HOH G:463 , HOH G:478 , MG G:500 , HOH G:1075
BINDING SITE FOR RESIDUE CAP G 600
14
BC5
SOFTWARE
KCX G:189 , ASP G:191 , GLU G:192 , CAP G:600
BINDING SITE FOR RESIDUE MG G 500
15
BC6
SOFTWARE
TRP A:55 , ASN A:111 , HOH A:1819 , LYS H:163 , LYS H:165 , KCX H:189 , ASP H:191 , GLU H:192 , HIS H:281 , ARG H:282 , HIS H:314 , LEU H:323 , SER H:367 , GLY H:368 , GLY H:369 , GLN H:389 , GLY H:391 , GLY H:392 , MG H:500 , HOH H:1277 , HOH H:1918
BINDING SITE FOR RESIDUE CAP H 600
16
BC7
SOFTWARE
KCX H:189 , ASP H:191 , GLU H:192 , CAP H:600
BINDING SITE FOR RESIDUE MG H 500
17
BC8
SOFTWARE
GLU E:49 , THR E:54 , TRP E:55 , ASN E:111 , HOH E:994 , 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 , HOH I:445 , HOH I:450 , HOH I:455 , MG I:500 , HOH I:540 , HOH I:995 , HOH I:1432
BINDING SITE FOR RESIDUE CAP I 600
18
BC9
SOFTWARE
ASN E:111 , KCX I:189 , ASP I:191 , GLU I:192 , CAP I:600
BINDING SITE FOR RESIDUE MG I 500
19
CC1
SOFTWARE
GLU D:49 , TRP D:55 , ASN D:111 , HOH D:1771 , 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 , HOH J:475 , HOH J:499 , MG J:500 , HOH J:1614 , HOH J:1792 , HOH J:1936
BINDING SITE FOR RESIDUE CAP J 600
20
CC2
SOFTWARE
KCX J:189 , ASP J:191 , GLU J:192 , CAP J:600
BINDING SITE FOR RESIDUE MG J 500
[
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, 20)
Info
All SCOP Domains
1a: SCOP_d3kdoa1 (A:9-135)
1b: SCOP_d3kdob1 (B:7-135)
1c: SCOP_d3kdoc1 (C:5-135)
1d: SCOP_d3kdod1 (D:8-135)
1e: SCOP_d3kdoe1 (E:5-135)
1f: SCOP_d3kdof1 (F:8-135)
1g: SCOP_d3kdog1 (G:8-135)
1h: SCOP_d3kdoh1 (H:7-135)
1i: SCOP_d3kdoi1 (I:7-135)
1j: SCOP_d3kdoj1 (J:7-135)
2a: SCOP_d3kdoa2 (A:136-444)
2b: SCOP_d3kdob2 (B:136-444)
2c: SCOP_d3kdoc2 (C:136-444)
2d: SCOP_d3kdod2 (D:136-444)
2e: SCOP_d3kdoe2 (E:136-444)
2f: SCOP_d3kdof2 (F:136-444)
2g: SCOP_d3kdog2 (G:136-444)
2h: SCOP_d3kdoh2 (H:136-444)
2i: SCOP_d3kdoi2 (I:136-444)
2j: SCOP_d3kdoj2 (J:136-444)
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
:
automated matches
(27)
Protein domain
:
automated matches
(27)
Thermococcus kodakaraensis [TaxId: 69014]
(2)
1a
d3kdoa1
A:9-135
1b
d3kdob1
B:7-135
1c
d3kdoc1
C:5-135
1d
d3kdod1
D:8-135
1e
d3kdoe1
E:5-135
1f
d3kdof1
F:8-135
1g
d3kdog1
G:8-135
1h
d3kdoh1
H:7-135
1i
d3kdoi1
I:7-135
1j
d3kdoj1
J:7-135
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
RuBisCo, C-terminal domain
(66)
Family
:
automated matches
(10)
Protein domain
:
automated matches
(10)
Thermococcus kodakaraensis [TaxId: 69014]
(2)
2a
d3kdoa2
A:136-444
2b
d3kdob2
B:136-444
2c
d3kdoc2
C:136-444
2d
d3kdod2
D:136-444
2e
d3kdoe2
E:136-444
2f
d3kdof2
F:136-444
2g
d3kdog2
G:136-444
2h
d3kdoh2
H:136-444
2i
d3kdoi2
I:136-444
2j
d3kdoj2
J:136-444
[
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
Chain C
Chain D
Chain E
Chain F
Chain G
Chain H
Chain I
Chain J
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 (722 KB)
Header - Asym.Unit
Biol.Unit 1 (711 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
3KDO
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help