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.
3AXM
Asym. Unit
Info
Asym.Unit (798 KB)
Biol.Unit 1 (787 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF RICE RUBISCO IN COMPLEX WITH 6PG
Authors
:
H. Matsumura, E. Mizohata, H. Ishida, A. Kogami, T. Ueno, A. Makino, T. I A. Yokota, T. Mae, Y. Kai
Date
:
11 Apr 11 (Deposition) - 11 Apr 12 (Release) - 05 Jun 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.65
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,S,T,U,V,W,X,Y,Z
Biol. Unit 1: A,B,C,D,E,F,G,H,S,T,U,V,W,X,Y,Z (1x)
Keywords
:
Alpha/Beta Barrel, Photosynthetic Carbon Reduction, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Matsumura, E. Mizohata, H. Ishida, A. Kogami, T. Ueno, A. Makino, T. Inoue, A. Yokota, T. Mae, Y. Kai
Crystal Structure Of Rice Rubisco And Implications For Activation Induced By Positive Effectors Nadph And 6-Phosphogluconate
J. Mol. Biol. V. 422 75 2012
[
close entry info
]
Hetero Components
(4, 32)
Info
All Hetero Components
1a: 6-PHOSPHOGLUCONIC ACID (6PGa)
1b: 6-PHOSPHOGLUCONIC ACID (6PGb)
1c: 6-PHOSPHOGLUCONIC ACID (6PGc)
1d: 6-PHOSPHOGLUCONIC ACID (6PGd)
1e: 6-PHOSPHOGLUCONIC ACID (6PGe)
1f: 6-PHOSPHOGLUCONIC ACID (6PGf)
1g: 6-PHOSPHOGLUCONIC ACID (6PGg)
1h: 6-PHOSPHOGLUCONIC ACID (6PGh)
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)
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)
4a: METHYLAMINE (NMEa)
4b: METHYLAMINE (NMEb)
4c: METHYLAMINE (NMEc)
4d: METHYLAMINE (NMEd)
4e: METHYLAMINE (NMEe)
4f: METHYLAMINE (NMEf)
4g: METHYLAMINE (NMEg)
4h: METHYLAMINE (NMEh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
6PG
8
Ligand/Ion
6-PHOSPHOGLUCONIC ACID
2
KCX
8
Mod. Amino Acid
LYSINE NZ-CARBOXYLIC ACID
3
MG
8
Ligand/Ion
MAGNESIUM ION
4
NME
8
Mod. Amino Acid
METHYLAMINE
[
close Hetero Component info
]
Sites
(16, 16)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
KCX A:201 , ASP A:203 , GLU A:204 , 6PG A:479 , HOH A:2934
BINDING SITE FOR RESIDUE MG A 478
02
AC2
SOFTWARE
THR A:173 , LYS A:175 , KCX A:201 , ASP A:203 , GLU A:204 , HIS A:294 , ARG A:295 , HIS A:298 , SER A:379 , MG A:478 , HOH A:497 , HOH A:498 , HOH A:884 , HOH A:1916 , HOH A:2402 , HOH A:2491 , HOH A:2648 , HOH A:2934 , HOH A:3580 , ASN B:123
BINDING SITE FOR RESIDUE 6PG A 479
03
AC3
SOFTWARE
KCX B:201 , ASP B:203 , GLU B:204 , 6PG B:479 , HOH B:2967
BINDING SITE FOR RESIDUE MG B 478
04
AC4
SOFTWARE
ASN A:123 , THR B:173 , LYS B:175 , KCX B:201 , ASP B:203 , GLU B:204 , HIS B:294 , ARG B:295 , HIS B:298 , SER B:379 , MG B:478 , HOH B:649 , HOH B:1425 , HOH B:1849 , HOH B:1984 , HOH B:2967 , HOH B:3286 , HOH B:3596 , HOH B:3597
BINDING SITE FOR RESIDUE 6PG B 479
05
AC5
SOFTWARE
KCX C:201 , ASP C:203 , GLU C:204 , 6PG C:479 , HOH C:481
BINDING SITE FOR RESIDUE MG C 478
06
AC6
SOFTWARE
LYS C:175 , KCX C:201 , ASP C:203 , GLU C:204 , HIS C:294 , ARG C:295 , HIS C:298 , SER C:379 , MG C:478 , HOH C:481 , HOH C:695 , HOH C:1439 , HOH C:1507 , HOH C:1962 , HOH C:2485 , HOH C:3592 , ASN D:123
BINDING SITE FOR RESIDUE 6PG C 479
07
AC7
SOFTWARE
KCX D:201 , ASP D:203 , GLU D:204 , 6PG D:479 , HOH D:3132
BINDING SITE FOR RESIDUE MG D 478
08
AC8
SOFTWARE
ASN C:123 , LYS D:175 , KCX D:201 , ASP D:203 , GLU D:204 , HIS D:294 , ARG D:295 , HIS D:298 , SER D:379 , MG D:478 , HOH D:1958 , HOH D:2156 , HOH D:2304 , HOH D:2356 , HOH D:3132 , HOH D:3437 , HOH D:3598
BINDING SITE FOR RESIDUE 6PG D 479
09
AC9
SOFTWARE
KCX E:201 , ASP E:203 , GLU E:204 , 6PG E:479 , HOH E:1908
BINDING SITE FOR RESIDUE MG E 478
10
BC1
SOFTWARE
THR E:173 , LYS E:175 , KCX E:201 , ASP E:203 , GLU E:204 , HIS E:294 , ARG E:295 , HIS E:298 , SER E:379 , MG E:478 , HOH E:512 , HOH E:794 , HOH E:1908 , HOH E:1929 , HOH E:2080 , HOH E:2752 , HOH E:3520 , ASN F:123
BINDING SITE FOR RESIDUE 6PG E 479
11
BC2
SOFTWARE
KCX F:201 , ASP F:203 , GLU F:204 , 6PG F:479 , HOH F:2817
BINDING SITE FOR RESIDUE MG F 478
12
BC3
SOFTWARE
ASN E:123 , HOH E:524 , HOH E:3356 , THR F:173 , LYS F:175 , KCX F:201 , ASP F:203 , GLU F:204 , HIS F:294 , ARG F:295 , HIS F:298 , GLY F:329 , SER F:379 , MG F:478 , HOH F:508 , HOH F:1401 , HOH F:1445 , HOH F:2795 , HOH F:2817 , HOH F:3601
BINDING SITE FOR RESIDUE 6PG F 479
13
BC4
SOFTWARE
KCX G:201 , ASP G:203 , GLU G:204 , 6PG G:479 , HOH G:1909
BINDING SITE FOR RESIDUE MG G 478
14
BC5
SOFTWARE
THR G:173 , LYS G:175 , KCX G:201 , ASP G:203 , GLU G:204 , HIS G:294 , ARG G:295 , HIS G:298 , SER G:379 , MG G:478 , HOH G:756 , HOH G:1909 , HOH G:3396 , HOH G:3584 , HOH G:3585 , HOH G:3586 , HOH G:3588 , ASN H:123 , HOH H:3483
BINDING SITE FOR RESIDUE 6PG G 479
15
BC6
SOFTWARE
KCX H:201 , ASP H:203 , GLU H:204 , 6PG H:479 , HOH H:3197
BINDING SITE FOR RESIDUE MG H 478
16
BC7
SOFTWARE
ASN G:123 , THR H:173 , LYS H:175 , KCX H:201 , ASP H:203 , GLU H:204 , HIS H:294 , ARG H:295 , HIS H:298 , GLY H:329 , SER H:379 , MG H:478 , HOH H:522 , HOH H:1446 , HOH H:2251 , HOH H:3197 , HOH H:3314 , HOH H:3604
BINDING SITE FOR RESIDUE 6PG H 479
[
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, 8)
Info
All PROSITE Patterns/Profiles
1: RUBISCO_LARGE (A:196-204,B:196-204,C:196-204,D:19...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RUBISCO_LARGE
PS00157
Ribulose bisphosphate carboxylase large chain active site.
RBL_ORYSJ
196-204
8
A:196-204
B:196-204
C:196-204
D:196-204
E:196-204
F:196-204
G:196-204
H:196-204
[
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, 24)
Info
All SCOP Domains
1a: SCOP_d3axma1 (A:12-150)
1b: SCOP_d3axmb1 (B:12-150)
1c: SCOP_d3axmc1 (C:12-150)
1d: SCOP_d3axmd1 (D:12-150)
1e: SCOP_d3axme1 (E:12-150)
1f: SCOP_d3axmf1 (F:12-150)
1g: SCOP_d3axmg1 (G:12-150)
1h: SCOP_d3axmh1 (H:12-150)
2a: SCOP_d3axms_ (S:)
2b: SCOP_d3axmt_ (T:)
2c: SCOP_d3axmu_ (U:)
2d: SCOP_d3axmv_ (V:)
2e: SCOP_d3axmw_ (W:)
2f: SCOP_d3axmx_ (X:)
2g: SCOP_d3axmy_ (Y:)
2h: SCOP_d3axmz_ (Z:)
3a: SCOP_d3axma2 (A:151-463)
3b: SCOP_d3axmb2 (B:151-463)
3c: SCOP_d3axmc2 (C:151-463)
3d: SCOP_d3axmd2 (D:151-463)
3e: SCOP_d3axme2 (E:151-463)
3f: SCOP_d3axmf2 (F:151-463)
3g: SCOP_d3axmg2 (G:151-463)
3h: SCOP_d3axmh2 (H:151-463)
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)
Rice (Oryza sativa) [TaxId: 4530]
(3)
1a
d3axma1
A:12-150
1b
d3axmb1
B:12-150
1c
d3axmc1
C:12-150
1d
d3axmd1
D:12-150
1e
d3axme1
E:12-150
1f
d3axmf1
F:12-150
1g
d3axmg1
G:12-150
1h
d3axmh1
H:12-150
Fold
:
RuBisCO, small subunit
(44)
Superfamily
:
RuBisCO, small subunit
(44)
Family
:
RuBisCO, small subunit
(44)
Protein domain
:
automated matches
(16)
Oryza sativa [TaxId: 39947]
(2)
2a
d3axms_
S:
2b
d3axmt_
T:
2c
d3axmu_
U:
2d
d3axmv_
V:
2e
d3axmw_
W:
2f
d3axmx_
X:
2g
d3axmy_
Y:
2h
d3axmz_
Z:
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)
Rice (Oryza sativa) [TaxId: 4530]
(3)
3a
d3axma2
A:151-463
3b
d3axmb2
B:151-463
3c
d3axmc2
C:151-463
3d
d3axmd2
D:151-463
3e
d3axme2
E:151-463
3f
d3axmf2
F:151-463
3g
d3axmg2
G:151-463
3h
d3axmh2
H:151-463
[
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 S
Chain T
Chain U
Chain V
Chain W
Chain X
Chain Y
Chain Z
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 (798 KB)
Header - Asym.Unit
Biol.Unit 1 (787 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
3AXM
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help