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1UPP
Asym. Unit
Info
Asym.Unit (399 KB)
Biol.Unit 1 (775 KB)
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(1)
Title
:
SPINACH RUBISCO IN COMPLEX WITH 2-CARBOXYARABINITOL 2 BISPHOSPHATE AND CALCIUM.
Authors
:
S. Karkehabadi, T. C. Taylor, I. Andersson
Date
:
09 Oct 03 (Deposition) - 14 Oct 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,C,E,G,I,J,K,L
Biol. Unit 1: A,C,E,G,I,J,K,L (2x)
Keywords
:
Lyase, Carbon-Carbon, Oxidoreductase, Photosynthesis, Carbon-Dioxide Fixation
(Keyword Search:
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Reference
:
S. Karehabadi, T. C. Taylor, I. Andersson
Calcium Supports Loop Closure But Not Catalysis In Rubisco
J. Mol. Biol. V. 334 65 2003
[
close entry info
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Hetero Components
(3, 12)
Info
All Hetero Components
2a: 2-CARBOXYARABINITOL-1,5-DIPHOSPHAT... (CAPa)
2b: 2-CARBOXYARABINITOL-1,5-DIPHOSPHAT... (CAPb)
2c: 2-CARBOXYARABINITOL-1,5-DIPHOSPHAT... (CAPc)
2d: 2-CARBOXYARABINITOL-1,5-DIPHOSPHAT... (CAPd)
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
3a: LYSINE NZ-CARBOXYLIC ACID (KCXa)
3b: LYSINE NZ-CARBOXYLIC ACID (KCXb)
3c: LYSINE NZ-CARBOXYLIC ACID (KCXc)
3d: LYSINE NZ-CARBOXYLIC ACID (KCXd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
4
Ligand/Ion
CALCIUM ION
2
CAP
4
Ligand/Ion
2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
3
KCX
4
Mod. Amino Acid
LYSINE NZ-CARBOXYLIC ACID
[
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Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
LYS A:175 , LYS A:177 , KCX A:201 , ASP A:203 , GLU A:204 , CAP A:477
BINDING SITE FOR RESIDUE CA A 476
2
AC2
SOFTWARE
LYS C:175 , LYS C:177 , KCX C:201 , ASP C:203 , GLU C:204 , CAP C:477
BINDING SITE FOR RESIDUE CA C 476
3
AC3
SOFTWARE
LYS E:177 , KCX E:201 , ASP E:203 , GLU E:204 , CAP E:477
BINDING SITE FOR RESIDUE CA E 476
4
AC4
SOFTWARE
LYS G:177 , KCX G:201 , ASP G:203 , GLU G:204 , CAP G:477
BINDING SITE FOR RESIDUE CA G 476
5
AC5
SOFTWARE
THR A:173 , LYS A:175 , LYS A:177 , KCX A:201 , GLU A:204 , HIS A:294 , ARG A:295 , HIS A:327 , LYS A:334 , LEU A:335 , SER A:379 , GLY A:380 , GLY A:381 , GLY A:403 , GLY A:404 , CA A:476 , HOH A:2070 , HOH A:2110 , HOH A:2111 , HOH A:2112 , GLU E:60 , THR E:65 , TRP E:66 , ASN E:123 , HOH E:2016
BINDING SITE FOR RESIDUE CAP A 477
6
AC6
SOFTWARE
GLU C:60 , THR C:65 , TRP C:66 , ASN C:123 , THR C:173 , LYS C:175 , LYS C:177 , KCX C:201 , HIS C:294 , ARG C:295 , HIS C:327 , LYS C:334 , LEU C:335 , SER C:379 , GLY C:380 , GLY C:381 , PHE C:402 , GLY C:403 , GLY C:404 , CA C:476 , HOH C:2082 , HOH C:2083 , HOH C:2105 , HOH C:2108
BINDING SITE FOR RESIDUE CAP C 477
7
AC7
SOFTWARE
GLU A:60 , THR A:65 , TRP A:66 , ASN A:123 , THR E:173 , LYS E:175 , LYS E:177 , KCX E:201 , HIS E:294 , 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 , CA E:476 , HOH E:2080 , HOH E:2081 , HOH E:2129 , HOH E:2130 , HOH E:2131 , HOH E:2132
BINDING SITE FOR RESIDUE CAP E 477
8
AC8
SOFTWARE
GLU G:60 , THR G:65 , TRP G:66 , ASN G:123 , THR G:173 , LYS G:175 , LYS G:177 , KCX G:201 , HIS G:294 , ARG G:295 , HIS G:327 , LYS G:334 , LEU G:335 , SER G:379 , GLY G:380 , GLY G:381 , GLY G:403 , GLY G:404 , CA G:476 , HOH G:2088 , HOH G:2104 , HOH G:2132 , HOH G:2133
BINDING SITE FOR RESIDUE CAP G 477
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: RUBISCO_LARGE (A:196-204,C:196-204,E:196-204,G:19...)
;
View:
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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
4
A:196-204
C:196-204
E:196-204
G:196-204
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(3, 12)
Info
All SCOP Domains
1a: SCOP_d1uppa1 (A:9-147)
1b: SCOP_d1uppc1 (C:9-147)
1c: SCOP_d1uppe1 (E:9-147)
1d: SCOP_d1uppg1 (G:9-147)
2a: SCOP_d1uppi_ (I:)
2b: SCOP_d1uppj_ (J:)
2c: SCOP_d1uppk_ (K:)
2d: SCOP_d1uppl_ (L:)
3a: SCOP_d1uppa2 (A:148-475)
3b: SCOP_d1uppc2 (C:148-475)
3c: SCOP_d1uppe2 (E:148-475)
3d: SCOP_d1uppg2 (G:148-475)
View:
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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
d1uppa1
A:9-147
1b
d1uppc1
C:9-147
1c
d1uppe1
E:9-147
1d
d1uppg1
G: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
d1uppi_
I:
2b
d1uppj_
J:
2c
d1uppk_
K:
2d
d1uppl_
L:
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
d1uppa2
A:148-475
3b
d1uppc2
C:148-475
3c
d1uppe2
E:148-475
3d
d1uppg2
G:148-475
[
close SCOP info
]
CATH Domains
(3, 12)
Info
all CATH domains
1a: CATH_1uppA01 (A:22-148)
1b: CATH_1uppC01 (C:22-148)
1c: CATH_1uppE01 (E:22-148)
1d: CATH_1uppG01 (G:22-148)
2a: CATH_1uppI00 (I:1-123)
2b: CATH_1uppJ00 (J:1-123)
2c: CATH_1uppK00 (K:1-123)
2d: CATH_1uppL00 (L:1-123)
3a: CATH_1uppA02 (A:149-462)
3b: CATH_1uppC02 (C:149-462)
3c: CATH_1uppE02 (E:149-462)
3d: CATH_1uppG02 (G: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
1uppA01
A:22-148
1b
1uppC01
C:22-148
1c
1uppE01
E:22-148
1d
1uppG01
G: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
1uppI00
I:1-123
2b
1uppJ00
J:1-123
2c
1uppK00
K:1-123
2d
1uppL00
L:1-123
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Rubisco
(49)
Spinach (Spinacia oleracea)
(10)
3a
1uppA02
A:149-462
3b
1uppC02
C:149-462
3c
1uppE02
E:149-462
3d
1uppG02
G:149-462
[
close CATH info
]
Pfam Domains
(3, 12)
Info
all PFAM domains
1a: PFAM_RuBisCO_large_1uppG01 (G:154-462)
1b: PFAM_RuBisCO_large_1uppG02 (G:154-462)
1c: PFAM_RuBisCO_large_1uppG03 (G:154-462)
1d: PFAM_RuBisCO_large_1uppG04 (G:154-462)
2a: PFAM_RuBisCO_large_N_1uppG05 (G:21-146)
2b: PFAM_RuBisCO_large_N_1uppG06 (G:21-146)
2c: PFAM_RuBisCO_large_N_1uppG07 (G:21-146)
2d: PFAM_RuBisCO_large_N_1uppG08 (G:21-146)
3a: PFAM_RuBisCO_small_1uppL01 (L:11-121)
3b: PFAM_RuBisCO_small_1uppL02 (L:11-121)
3c: PFAM_RuBisCO_small_1uppL03 (L:11-121)
3d: PFAM_RuBisCO_small_1uppL04 (L:11-121)
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Clans
(
)
(
)
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(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: RuBisCO_large]
(36)
Family
:
RuBisCO_large
(36)
Spinacia oleracea (Spinach)
(6)
1a
RuBisCO_large-1uppG01
G:154-462
1b
RuBisCO_large-1uppG02
G:154-462
1c
RuBisCO_large-1uppG03
G:154-462
1d
RuBisCO_large-1uppG04
G:154-462
Clan
:
no clan defined [family: RuBisCO_large_N]
(27)
Family
:
RuBisCO_large_N
(27)
Spinacia oleracea (Spinach)
(6)
2a
RuBisCO_large_N-1uppG05
G:21-146
2b
RuBisCO_large_N-1uppG06
G:21-146
2c
RuBisCO_large_N-1uppG07
G:21-146
2d
RuBisCO_large_N-1uppG08
G:21-146
Clan
:
no clan defined [family: RuBisCO_small]
(23)
Family
:
RuBisCO_small
(23)
Spinacia oleracea (Spinach)
(6)
3a
RuBisCO_small-1uppL01
L:11-121
3b
RuBisCO_small-1uppL02
L:11-121
3c
RuBisCO_small-1uppL03
L:11-121
3d
RuBisCO_small-1uppL04
L:11-121
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