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Asym. Unit
Info
Asym.Unit (412 KB)
Biol.Unit 1 (799 KB)
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(1)
Title
:
ACTIVATED RIBULOSE 1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE (RUBISCO) COMPLEXED WITH THE REACTION INTERMEDIATE ANALOGUE 2-CARBOXYARABINITOL 1,5-BISPHOSPHATE
Authors
:
H. Sugawara, H. Yamamoto, N. Shibata, T. Inoue, C. Miyake, A. Yokota, Y.
Date
:
29 Sep 98 (Deposition) - 27 Sep 99 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,C,E,G,S,U,W,Y
Biol. Unit 1: A,C,E,G,S,U,W,Y (2x)
Keywords
:
Carbon Dioxide Fixation, Complex (Rubisco-Reaction Intermediate), High Specificity Factor, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Sugawara, H. Yamamoto, N. Shibata, T. Inoue, S. Okada, C. Miyake, A. Yokota, Y. Kai
Crystal Structure Of Carboxylase Reaction-Oriented Ribulose 1, 5-Bisphosphate Carboxylase/Oxygenase From A Thermophilic Red Alga, Galdieria Partita.
J. Biol. Chem. V. 274 15655 1999
(for further references see the
PDB file header
)
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Hetero Components
(3, 12)
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)
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: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CAP
4
Ligand/Ion
2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
2
KCX
4
Mod. Amino Acid
LYSINE NZ-CARBOXYLIC ACID
3
MG
4
Ligand/Ion
MAGNESIUM ION
[
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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: MGA (AUTHOR)
10: MGC (AUTHOR)
11: MGE (AUTHOR)
12: MGG (AUTHOR)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
KCX A:201 , ASP A:203 , GLU A:204 , CAP A:491
BINDING SITE FOR RESIDUE MG A 490
02
AC2
SOFTWARE
KCX C:201 , ASP C:203 , GLU C:204 , CAP C:491
BINDING SITE FOR RESIDUE MG C 490
03
AC3
SOFTWARE
KCX E:201 , ASP E:203 , GLU E:204 , CAP E:491
BINDING SITE FOR RESIDUE MG E 490
04
AC4
SOFTWARE
THR G:173 , KCX G:201 , ASP G:203 , GLU G:204 , CAP G:491
BINDING SITE FOR RESIDUE MG G 490
05
AC5
SOFTWARE
THR A:173 , LYS A:175 , LYS A:177 , KCX A:201 , ASP A:203 , 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 , MG A:490 , HOH A:518 , HOH A:554 , HOH A:561 , HOH A:565 , HOH A:572 , HOH A:584 , GLU C:60 , THR C:65 , TRP C:66 , ASN C:123
BINDING SITE FOR RESIDUE CAP A 491
06
AC6
SOFTWARE
GLU A:60 , THR A:65 , TRP A:66 , ASN A:123 , THR C:173 , LYS C:175 , LYS C:177 , KCX C:201 , ASP C:203 , GLU C:204 , HIS C:294 , ARG C:295 , HIS C:327 , LYS C:334 , LEU C:335 , SER C:379 , GLY C:380 , GLY C:381 , GLY C:403 , GLY C:404 , MG C:490 , HOH C:525 , HOH C:555 , HOH C:564 , HOH C:575 , HOH C:580
BINDING SITE FOR RESIDUE CAP C 491
07
AC7
SOFTWARE
THR E:173 , LYS E:175 , LYS E:177 , KCX E:201 , ASP E:203 , GLU E:204 , 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 , MG E:490 , HOH E:520 , HOH E:555 , HOH E:562 , HOH E:566 , HOH E:572 , HOH E:580 , GLU G:60 , THR G:65 , TRP G:66 , ASN G:123
BINDING SITE FOR RESIDUE CAP E 491
08
AC8
SOFTWARE
GLU E:60 , THR E:65 , TRP E:66 , ASN E:123 , THR G:173 , LYS G:175 , LYS G:177 , KCX G:201 , ASP G:203 , GLU G:204 , 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 , MG G:490 , HOH G:525 , HOH G:555 , HOH G:564 , HOH G:577 , HOH G:581
BINDING SITE FOR RESIDUE CAP G 491
09
MGA
AUTHOR
KCX A:201 , ASP A:203 , GLU A:204 , CAP A:491
MG BINDING SITE CHAIN A
10
MGC
AUTHOR
KCX E:201 , ASP E:203 , GLU E:204 , CAP C:491
MG BINDING SITE CHAIN C
11
MGE
AUTHOR
KCX E:201 , ASP E:203 , GLU E:204 , CAP E:491
MG BINDING SITE CHAIN E
12
MGG
AUTHOR
KCX G:201 , ASP G:203 , GLU G:204 , CAP G:491
MG BINDING SITE CHAIN G
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
Info
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Exons
(0, 0)
Info
All Exons
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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_d1bwva2 (A:7-149)
1b: SCOP_d1bwvc2 (C:7-149)
1c: SCOP_d1bwve2 (E:7-149)
1d: SCOP_d1bwvg2 (G:7-149)
2a: SCOP_d1bwvs_ (S:)
2b: SCOP_d1bwvu_ (U:)
2c: SCOP_d1bwvw_ (W:)
2d: SCOP_d1bwvy_ (Y:)
3a: SCOP_d1bwva1 (A:150-478)
3b: SCOP_d1bwvc1 (C:150-478)
3c: SCOP_d1bwve1 (E:150-478)
3d: SCOP_d1bwvg1 (G:150-478)
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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)
Galdieria partita [TaxId: 83374]
(2)
1a
d1bwva2
A:7-149
1b
d1bwvc2
C:7-149
1c
d1bwve2
E:7-149
1d
d1bwvg2
G:7-149
Fold
:
RuBisCO, small subunit
(44)
Superfamily
:
RuBisCO, small subunit
(44)
Family
:
RuBisCO, small subunit
(44)
Protein domain
:
Ribulose 1,5-bisphosphate carboxylase-oxygenase
(28)
Galdieria partita [TaxId: 83374]
(2)
2a
d1bwvs_
S:
2b
d1bwvu_
U:
2c
d1bwvw_
W:
2d
d1bwvy_
Y:
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)
Galdieria partita [TaxId: 83374]
(2)
3a
d1bwva1
A:150-478
3b
d1bwvc1
C:150-478
3c
d1bwve1
E:150-478
3d
d1bwvg1
G:150-478
[
close SCOP info
]
CATH Domains
(3, 12)
Info
all CATH domains
1a: CATH_1bwvA01 (A:22-148)
1b: CATH_1bwvC01 (C:22-148)
1c: CATH_1bwvE01 (E:22-148)
1d: CATH_1bwvG01 (G:22-148)
2a: CATH_1bwvS00 (S:8-155)
2b: CATH_1bwvU00 (U:8-155)
2c: CATH_1bwvW00 (W:8-155)
2d: CATH_1bwvY00 (Y:8-155)
3a: CATH_1bwvA02 (A:149-462)
3b: CATH_1bwvC02 (C:149-462)
3c: CATH_1bwvE02 (E:149-462)
3d: CATH_1bwvG02 (G:149-462)
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)
(
)
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)
Galdieria partita. Organism_taxid: 83374.
(1)
1a
1bwvA01
A:22-148
1b
1bwvC01
C:22-148
1c
1bwvE01
E:22-148
1d
1bwvG01
G:22-148
Topology
:
Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase
(42)
Homologous Superfamily
:
[code=3.30.190.10, no name defined]
(35)
Galdieria partita. Organism_taxid: 83374.
(1)
2a
1bwvS00
S:8-155
2b
1bwvU00
U:8-155
2c
1bwvW00
W:8-155
2d
1bwvY00
Y:8-155
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Rubisco
(49)
Galdieria partita. Organism_taxid: 83374.
(1)
3a
1bwvA02
A:149-462
3b
1bwvC02
C:149-462
3c
1bwvE02
E:149-462
3d
1bwvG02
G:149-462
[
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Pfam Domains
(0, 0)
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