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1RXO
Biol. Unit 1
Info
Asym.Unit (396 KB)
Biol.Unit 1 (774 KB)
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(1)
Title
:
ACTIVATED SPINACH RUBISCO IN COMPLEX WITH ITS SUBSTRATE RIBULOSE-1,5-BISPHOSPHATE AND CALCIUM
Authors
:
T. C. Taylor, I. Andersson
Date
:
06 Dec 96 (Deposition) - 16 Jun 97 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
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, I. Andersson
The Structure Of The Complex Between Rubisco And Its Natura Substrate Ribulose 1, 5-Bisphosphate.
J. Mol. Biol. V. 265 432 1997
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 16)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
2a: LYSINE NZ-CARBOXYLIC ACID (KCXa)
2b: LYSINE NZ-CARBOXYLIC ACID (KCXb)
2c: LYSINE NZ-CARBOXYLIC ACID (KCXc)
2d: LYSINE NZ-CARBOXYLIC ACID (KCXd)
3a: RIBULOSE-1,5-DIPHOSPHATE (RUBa)
3b: RIBULOSE-1,5-DIPHOSPHATE (RUBb)
3c: RIBULOSE-1,5-DIPHOSPHATE (RUBc)
3d: RIBULOSE-1,5-DIPHOSPHATE (RUBd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
KCX
8
Mod. Amino Acid
LYSINE NZ-CARBOXYLIC ACID
3
RUB
8
Ligand/Ion
RIBULOSE-1,5-DIPHOSPHATE
[
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]
Sites
(12, 12)
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: ACB (UNKNOWN)
10: ACE (UNKNOWN)
11: ACH (UNKNOWN)
12: ACL (UNKNOWN)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TRP E:66 , LYS L:175 , KCX L:201 , GLU L:204 , HIS L:294 , ARG L:295 , HIS L:298 , SER L:379 , GLY L:380 , GLY L:381 , GLY L:403 , GLY L:404 , CA L:477 , HOH L:525 , HOH L:526 , HOH L:541 , HOH L:562 , HOH L:568 , HOH L:593 , HOH L:619 , HOH L:660
BINDING SITE FOR RESIDUE RUB L 476
02
AC2
SOFTWARE
TRP B:66 , LYS B:175 , KCX B:201 , GLU B:204 , HIS B:294 , ARG B:295 , HIS B:298 , SER B:379 , GLY B:380 , GLY B:381 , GLY B:403 , GLY B:404 , CA B:477 , HOH B:526 , HOH B:527 , HOH B:542 , HOH B:563 , HOH B:569 , HOH B:594 , HOH B:620 , HOH B:661
BINDING SITE FOR RESIDUE RUB B 476
03
AC3
SOFTWARE
LYS E:175 , KCX E:201 , GLU E:204 , HIS E:294 , ARG E:295 , HIS E:298 , SER E:379 , GLY E:380 , GLY E:381 , GLY E:403 , GLY E:404 , CA E:477 , HOH E:566 , HOH E:567 , HOH E:583 , HOH E:606 , HOH E:613 , HOH E:638 , HOH E:665 , HOH E:709 , TRP L:66
BINDING SITE FOR RESIDUE RUB E 476
04
AC4
SOFTWARE
TRP H:66 , LYS H:175 , KCX H:201 , GLU H:204 , HIS H:294 , ARG H:295 , HIS H:298 , SER H:379 , GLY H:380 , GLY H:381 , GLY H:403 , GLY H:404 , CA H:477 , HOH H:528 , HOH H:529 , HOH H:544 , HOH H:565 , HOH H:571 , HOH H:596 , HOH H:622 , HOH H:663
BINDING SITE FOR RESIDUE RUB H 476
05
AC5
SOFTWARE
KCX L:201 , ASP L:203 , GLU L:204 , RUB L:476 , HOH L:583
BINDING SITE FOR RESIDUE CA L 477
06
AC6
SOFTWARE
KCX B:201 , ASP B:203 , GLU B:204 , RUB B:476 , HOH B:584
BINDING SITE FOR RESIDUE CA B 477
07
AC7
SOFTWARE
KCX E:201 , ASP E:203 , GLU E:204 , RUB E:476 , HOH E:628
BINDING SITE FOR RESIDUE CA E 477
08
AC8
SOFTWARE
KCX H:201 , ASP H:203 , GLU H:204 , RUB H:476 , HOH H:586
BINDING SITE FOR RESIDUE CA H 477
09
ACB
UNKNOWN
KCX B:201 , ASP B:203 , GLU B:204
ACTIVE SITE.
10
ACE
UNKNOWN
KCX E:201 , ASP E:203 , GLU E:204
ACTIVE SITE.
11
ACH
UNKNOWN
KCX H:201 , ASP H:203 , GLU H:204
ACTIVE SITE.
12
ACL
UNKNOWN
KCX 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
[
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]
Exons
(0, 0)
Info
All Exons
View:
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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_d1rxob2 (B:9-147)
1b: SCOP_d1rxoe2 (E:9-147)
1c: SCOP_d1rxoh2 (H:9-147)
1d: SCOP_d1rxol2 (L:9-147)
2a: SCOP_d1rxoc_ (C:)
2b: SCOP_d1rxof_ (F:)
2c: SCOP_d1rxoi_ (I:)
2d: SCOP_d1rxos_ (S:)
3a: SCOP_d1rxob1 (B:148-463)
3b: SCOP_d1rxoe1 (E:148-463)
3c: SCOP_d1rxoh1 (H:148-463)
3d: SCOP_d1rxol1 (L:148-463)
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)
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(
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)
(
)
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(
)
(
)
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
d1rxob2
B:9-147
1b
d1rxoe2
E:9-147
1c
d1rxoh2
H:9-147
1d
d1rxol2
L: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
d1rxoc_
C:
2b
d1rxof_
F:
2c
d1rxoi_
I:
2d
d1rxos_
S:
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
d1rxob1
B:148-463
3b
d1rxoe1
E:148-463
3c
d1rxoh1
H:148-463
3d
d1rxol1
L:148-463
[
close SCOP info
]
CATH Domains
(3, 12)
Info
all CATH domains
1a: CATH_1rxoB01 (B:22-148)
1b: CATH_1rxoE01 (E:22-148)
1c: CATH_1rxoH01 (H:22-148)
1d: CATH_1rxoL01 (L:22-148)
2a: CATH_1rxoC00 (C:1-123)
2b: CATH_1rxoF00 (F:1-123)
2c: CATH_1rxoI00 (I:1-123)
2d: CATH_1rxoS00 (S:1-123)
3a: CATH_1rxoB02 (B:149-462)
3b: CATH_1rxoE02 (E:149-462)
3c: CATH_1rxoH02 (H:149-462)
3d: CATH_1rxoL02 (L:149-462)
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)
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
1rxoB01
B:22-148
1b
1rxoE01
E:22-148
1c
1rxoH01
H:22-148
1d
1rxoL01
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
1rxoC00
C:1-123
2b
1rxoF00
F:1-123
2c
1rxoI00
I:1-123
2d
1rxoS00
S:1-123
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Rubisco
(49)
Spinach (Spinacia oleracea)
(10)
3a
1rxoB02
B:149-462
3b
1rxoE02
E:149-462
3c
1rxoH02
H:149-462
3d
1rxoL02
L:149-462
[
close CATH info
]
Pfam Domains
(3, 12)
Info
all PFAM domains
1a: PFAM_RuBisCO_large_1rxoL01 (L:154-462)
1b: PFAM_RuBisCO_large_1rxoL02 (L:154-462)
1c: PFAM_RuBisCO_large_1rxoL03 (L:154-462)
1d: PFAM_RuBisCO_large_1rxoL04 (L:154-462)
2a: PFAM_RuBisCO_large_N_1rxoL05 (L:21-146)
2b: PFAM_RuBisCO_large_N_1rxoL06 (L:21-146)
2c: PFAM_RuBisCO_large_N_1rxoL07 (L:21-146)
2d: PFAM_RuBisCO_large_N_1rxoL08 (L:21-146)
3a: PFAM_RuBisCO_small_1rxoS01 (S:11-121)
3b: PFAM_RuBisCO_small_1rxoS02 (S:11-121)
3c: PFAM_RuBisCO_small_1rxoS03 (S:11-121)
3d: PFAM_RuBisCO_small_1rxoS04 (S:11-121)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: RuBisCO_large]
(36)
Family
:
RuBisCO_large
(36)
Spinacia oleracea (Spinach)
(6)
1a
RuBisCO_large-1rxoL01
L:154-462
1b
RuBisCO_large-1rxoL02
L:154-462
1c
RuBisCO_large-1rxoL03
L:154-462
1d
RuBisCO_large-1rxoL04
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-1rxoL05
L:21-146
2b
RuBisCO_large_N-1rxoL06
L:21-146
2c
RuBisCO_large_N-1rxoL07
L:21-146
2d
RuBisCO_large_N-1rxoL08
L:21-146
Clan
:
no clan defined [family: RuBisCO_small]
(23)
Family
:
RuBisCO_small
(23)
Spinacia oleracea (Spinach)
(6)
3a
RuBisCO_small-1rxoS01
S:11-121
3b
RuBisCO_small-1rxoS02
S:11-121
3c
RuBisCO_small-1rxoS03
S:11-121
3d
RuBisCO_small-1rxoS04
S:11-121
[
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