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...
Getting 'PROSITE' information from database.
1RBO
Biol. Unit 1
Info
Asym.Unit (400 KB)
Biol.Unit 1 (782 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
SPINACH RUBISCO IN COMPLEX WITH THE INHIBITOR 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
Authors
:
T. C. Taylor, I. Andersson
Date
:
31 Oct 96 (Deposition) - 12 Mar 97 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : B,C,E,F,H,I,L,S
Biol. Unit 1: B,C,E,F,H,I,L,S (2x)
Keywords
:
Lyase, Carbon-Carbon
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. C. Taylor, M. D. Fothergill, I. Andersson
A Common Structural Basis For The Inhibition Of Ribulose 1, 5-Bisphosphate Carboxylase By 4-Carboxyarabinitol 1, 5-Bisphosphate And Xylulose 1, 5-Bisphosphate.
J. Biol. Chem. V. 271 32894 1996
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 8)
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)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CAP
8
Ligand/Ion
2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
[
close Hetero Component info
]
Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: ACB (UNKNOWN)
6: ACE (UNKNOWN)
7: ACH (UNKNOWN)
8: ACL (UNKNOWN)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLU E:60 , THR E:65 , TRP E:66 , ASN E:123 , THR L:173 , LYS L:175 , LYS L:177 , ASP L:203 , GLU L:204 , ARG L:295 , HIS L:327 , LYS L:334 , LEU L:335 , SER L:379 , GLY L:380 , GLY L:381 , GLY L:403 , GLY L:404 , HOH L:498 , HOH L:501 , HOH L:549 , HOH L:561 , HOH L:584 , HOH L:626 , HOH L:633 , HOH L:651
BINDING SITE FOR RESIDUE CAP L 476
2
AC2
SOFTWARE
GLU B:60 , THR B:65 , TRP B:66 , ASN B:123 , THR B:173 , LYS B:175 , LYS B:177 , ASP B:203 , GLU B:204 , ARG B:295 , HIS B:327 , LYS B:334 , LEU B:335 , SER B:379 , GLY B:380 , GLY B:381 , GLY B:403 , GLY B:404 , HOH B:501 , HOH B:504 , HOH B:552 , HOH B:564 , HOH B:586 , HOH B:628 , HOH B:635 , HOH B:653
BINDING SITE FOR RESIDUE CAP B 476
3
AC3
SOFTWARE
THR E:173 , LYS E:175 , LYS E:177 , ASP E:203 , GLU E:204 , ARG E:295 , HIS E:327 , LYS E:334 , LEU E:335 , SER E:379 , GLY E:380 , GLY E:381 , GLY E:403 , GLY E:404 , HOH E:501 , HOH E:504 , HOH E:552 , HOH E:564 , HOH E:587 , HOH E:629 , HOH E:636 , HOH E:654 , GLU L:60 , THR L:65 , TRP L:66 , ASN L:123
BINDING SITE FOR RESIDUE CAP E 476
4
AC4
SOFTWARE
GLU H:60 , THR H:65 , TRP H:66 , ASN H:123 , THR H:173 , LYS H:175 , LYS H:177 , ASP H:203 , GLU H:204 , ARG H:295 , HIS H:327 , LYS H:334 , LEU H:335 , SER H:379 , GLY H:380 , GLY H:381 , GLY H:403 , GLY H:404 , HOH H:502 , HOH H:505 , HOH H:553 , HOH H:565 , HOH H:587 , HOH H:629 , HOH H:636 , HOH H:654
BINDING SITE FOR RESIDUE CAP H 476
5
ACB
UNKNOWN
LYS B:201 , ASP B:203 , GLU B:204
ACTIVE SITE
6
ACE
UNKNOWN
LYS E:201 , ASP E:203 , GLU E:204
ACTIVE SITE
7
ACH
UNKNOWN
LYS H:201 , ASP H:203 , GLU H:204
ACTIVE SITE
8
ACL
UNKNOWN
LYS L:201 , ASP L:203 , GLU L:204
ACTIVE SITE
[
close Site info
]
SAPs(SNPs)/Variants
(1, 8)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_RBS1_SPIOL_001 (Y94Y, chain C/F/I/S, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_RBS1_SPIOL_001
*
P
94
Y
RBS1_SPIOL
---
---
C/F/I/S
Y
94
Y
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 8)
Info
All PROSITE Patterns/Profiles
1: RUBISCO_LARGE (B:196-204,E:196-204,H:196-204,L: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_SPIOL
196-204
8
B:196-204
E:196-204
H:196-204
L: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.
(no "Exon" information available for biological units yet)
SCOP Domains
(3, 12)
Info
All SCOP Domains
1a: SCOP_d1rbob2 (B:9-147)
1b: SCOP_d1rboh2 (H:9-147)
1c: SCOP_d1rbol2 (L:9-147)
1d: SCOP_d1rboe2 (E:9-147)
2a: SCOP_d1rboc_ (C:)
2b: SCOP_d1rboi_ (I:)
2c: SCOP_d1rbos_ (S:)
2d: SCOP_d1rbof_ (F:)
3a: SCOP_d1rbob1 (B:148-475)
3b: SCOP_d1rboh1 (H:148-475)
3c: SCOP_d1rbol1 (L:148-475)
3d: SCOP_d1rboe1 (E:148-475)
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)
Spinach (Spinacia oleracea) [TaxId: 3562]
(10)
1a
d1rbob2
B:9-147
1b
d1rboh2
H:9-147
1c
d1rbol2
L:9-147
1d
d1rboe2
E:9-147
Fold
:
RuBisCO, small subunit
(44)
Superfamily
:
RuBisCO, small subunit
(44)
Family
:
RuBisCO, small subunit
(44)
Protein domain
:
Ribulose 1,5-bisphosphate carboxylase-oxygenase
(28)
Spinach (Spinacia oleracea) [TaxId: 3562]
(10)
2a
d1rboc_
C:
2b
d1rboi_
I:
2c
d1rbos_
S:
2d
d1rbof_
F:
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)
Spinach (Spinacia oleracea) [TaxId: 3562]
(10)
3a
d1rbob1
B:148-475
3b
d1rboh1
H:148-475
3c
d1rbol1
L:148-475
3d
d1rboe1
E:148-475
[
close SCOP info
]
CATH Domains
(3, 12)
Info
all CATH domains
1a: CATH_1rboB01 (B:22-148)
1b: CATH_1rboE01 (E:22-148)
1c: CATH_1rboH01 (H:22-148)
1d: CATH_1rboL01 (L:22-148)
2a: CATH_1rboC00 (C:1-123)
2b: CATH_1rboF00 (F:1-123)
2c: CATH_1rboI00 (I:1-123)
2d: CATH_1rboS00 (S:1-123)
3a: CATH_1rboB02 (B:149-462)
3b: CATH_1rboE02 (E:149-462)
3c: CATH_1rboH02 (H:149-462)
3d: CATH_1rboL02 (L:149-462)
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)
Spinach (Spinacia oleracea)
(10)
1a
1rboB01
B:22-148
1b
1rboE01
E:22-148
1c
1rboH01
H:22-148
1d
1rboL01
L:22-148
Topology
:
Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase
(42)
Homologous Superfamily
:
[code=3.30.190.10, no name defined]
(35)
Spinach (Spinacia oleracea)
(10)
2a
1rboC00
C:1-123
2b
1rboF00
F:1-123
2c
1rboI00
I:1-123
2d
1rboS00
S:1-123
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Rubisco
(49)
Spinach (Spinacia oleracea)
(10)
3a
1rboB02
B:149-462
3b
1rboE02
E:149-462
3c
1rboH02
H:149-462
3d
1rboL02
L:149-462
[
close CATH info
]
Pfam Domains
(3, 12)
Info
all PFAM domains
1a: PFAM_RuBisCO_large_1rboL01 (L:154-462)
1b: PFAM_RuBisCO_large_1rboL02 (L:154-462)
1c: PFAM_RuBisCO_large_1rboL03 (L:154-462)
1d: PFAM_RuBisCO_large_1rboL04 (L:154-462)
2a: PFAM_RuBisCO_large_N_1rboL05 (L:21-146)
2b: PFAM_RuBisCO_large_N_1rboL06 (L:21-146)
2c: PFAM_RuBisCO_large_N_1rboL07 (L:21-146)
2d: PFAM_RuBisCO_large_N_1rboL08 (L:21-146)
3a: PFAM_RuBisCO_small_1rboS01 (S:11-121)
3b: PFAM_RuBisCO_small_1rboS02 (S:11-121)
3c: PFAM_RuBisCO_small_1rboS03 (S:11-121)
3d: PFAM_RuBisCO_small_1rboS04 (S:11-121)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: RuBisCO_large]
(36)
Family
:
RuBisCO_large
(36)
Spinacia oleracea (Spinach)
(6)
1a
RuBisCO_large-1rboL01
L:154-462
1b
RuBisCO_large-1rboL02
L:154-462
1c
RuBisCO_large-1rboL03
L:154-462
1d
RuBisCO_large-1rboL04
L:154-462
Clan
:
no clan defined [family: RuBisCO_large_N]
(27)
Family
:
RuBisCO_large_N
(27)
Spinacia oleracea (Spinach)
(6)
2a
RuBisCO_large_N-1rboL05
L:21-146
2b
RuBisCO_large_N-1rboL06
L:21-146
2c
RuBisCO_large_N-1rboL07
L:21-146
2d
RuBisCO_large_N-1rboL08
L:21-146
Clan
:
no clan defined [family: RuBisCO_small]
(23)
Family
:
RuBisCO_small
(23)
Spinacia oleracea (Spinach)
(6)
3a
RuBisCO_small-1rboS01
S:11-121
3b
RuBisCO_small-1rboS02
S:11-121
3c
RuBisCO_small-1rboS03
S:11-121
3d
RuBisCO_small-1rboS04
S:11-121
[
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 B
Chain C
Chain E
Chain F
Chain H
Chain I
Chain L
Chain S
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 (400 KB)
Header - Asym.Unit
Biol.Unit 1 (782 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
1RBO
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help