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1RCX
Asym. Unit
Info
Asym.Unit (791 KB)
Biol.Unit 1 (785 KB)
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(1)
Title
:
NON-ACTIVATED SPINACH RUBISCO IN COMPLEX WITH ITS SUBSTRATE RIBULOSE-1,5-BISPHOSPHATE
Authors
:
T. C. Taylor, I. Andersson
Date
:
06 Dec 96 (Deposition) - 16 Jun 97 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : B,C,E,F,H,I,K,L,M,O,P,R,S,T,V,W
Biol. Unit 1: B,C,E,F,H,I,K,L,M,O,P,R,S,T,V,W (1x)
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 Natural 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
(1, 8)
Info
All Hetero Components
1a: RIBULOSE-1,5-DIPHOSPHATE (RUBa)
1b: RIBULOSE-1,5-DIPHOSPHATE (RUBb)
1c: RIBULOSE-1,5-DIPHOSPHATE (RUBc)
1d: RIBULOSE-1,5-DIPHOSPHATE (RUBd)
1e: RIBULOSE-1,5-DIPHOSPHATE (RUBe)
1f: RIBULOSE-1,5-DIPHOSPHATE (RUBf)
1g: RIBULOSE-1,5-DIPHOSPHATE (RUBg)
1h: RIBULOSE-1,5-DIPHOSPHATE (RUBh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
RUB
8
Ligand/Ion
RIBULOSE-1,5-DIPHOSPHATE
[
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: ACB (UNKNOWN)
10: ACE (UNKNOWN)
11: ACH (UNKNOWN)
12: ACK (UNKNOWN)
13: ACL (UNKNOWN)
14: ACO (UNKNOWN)
15: ACR (UNKNOWN)
16: ACV (UNKNOWN)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR B:65 , TRP B:66 , ASN B:123 , HOH B:484 , THR L:173 , LYS L:175 , LYS L:201 , GLU L:204 , HIS L:294 , 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:505 , HOH L:583
BINDING SITE FOR RESIDUE RUB L 476
02
AC2
SOFTWARE
THR B:173 , LYS B:175 , LYS B:201 , GLU B:204 , HIS B:294 , 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:514 , HOH B:593 , THR L:65 , TRP L:66 , ASN L:123 , HOH L:633
BINDING SITE FOR RESIDUE RUB B 476
03
AC3
SOFTWARE
THR E:173 , LYS E:175 , LYS E:201 , 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 , HOH E:510 , HOH E:588 , THR H:65 , TRP H:66 , ASN H:123 , HOH H:495
BINDING SITE FOR RESIDUE RUB E 476
04
AC4
SOFTWARE
THR E:65 , TRP E:66 , ASN E:123 , HOH E:639 , THR H:173 , LYS H:175 , LYS H:201 , GLU H:204 , HIS H:294 , 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:525 , HOH H:603
BINDING SITE FOR RESIDUE RUB H 476
05
AC5
SOFTWARE
THR K:173 , LYS K:175 , LYS K:201 , GLU K:204 , HIS K:294 , ARG K:295 , HIS K:327 , LYS K:334 , LEU K:335 , SER K:379 , GLY K:380 , GLY K:381 , GLY K:403 , GLY K:404 , HOH K:509 , HOH K:588 , THR O:65 , TRP O:66 , ASN O:123 , HOH O:1104
BINDING SITE FOR RESIDUE RUB K 476
06
AC6
SOFTWARE
THR K:65 , TRP K:66 , ASN K:123 , HOH K:639 , THR O:173 , LYS O:175 , LYS O:201 , GLU O:204 , HIS O:294 , ARG O:295 , HIS O:327 , LYS O:334 , LEU O:335 , SER O:379 , GLY O:380 , GLY O:381 , GLY O:403 , GLY O:404 , HOH O:1152 , HOH O:1263
BINDING SITE FOR RESIDUE RUB O 476
07
AC7
SOFTWARE
THR R:173 , LYS R:175 , LYS R:201 , GLU R:204 , HIS R:294 , ARG R:295 , HIS R:327 , LYS R:334 , LEU R:335 , SER R:379 , GLY R:380 , GLY R:381 , GLY R:403 , GLY R:404 , HOH R:518 , HOH R:596 , THR V:65 , TRP V:66 , ASN V:123 , HOH V:497
BINDING SITE FOR RESIDUE RUB R 476
08
AC8
SOFTWARE
THR R:65 , TRP R:66 , ASN R:123 , HOH R:646 , THR V:173 , LYS V:175 , LYS V:201 , GLU V:204 , HIS V:294 , ARG V:295 , HIS V:327 , LYS V:334 , LEU V:335 , SER V:379 , GLY V:380 , GLY V:381 , GLY V:403 , GLY V:404 , HOH V:527 , HOH V:605
BINDING SITE FOR RESIDUE RUB V 476
09
ACB
UNKNOWN
LYS B:201 , ASP B:203 , GLU B:204
ACTIVE SITE
10
ACE
UNKNOWN
LYS E:201 , ASP E:203 , GLU E:204
ACTIVE SITE
11
ACH
UNKNOWN
LYS H:201 , ASP H:203 , GLU H:204
ACTIVE SITE
12
ACK
UNKNOWN
LYS K:201 , ASP K:203 , GLU K:204
ACTIVE SITE
13
ACL
UNKNOWN
LYS L:201 , ASP L:203 , GLU L:204
ACTIVE SITE
14
ACO
UNKNOWN
LYS O:201 , ASP O:203 , GLU O:204
ACTIVE SITE
15
ACR
UNKNOWN
LYS R:201 , ASP R:203 , GLU R:204
ACTIVE SITE
16
ACV
UNKNOWN
LYS V:201 , ASP V:203 , GLU V:204
ACTIVE SITE
[
close Site info
]
SAPs(SNPs)/Variants
(1, 8)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_RBS1_SPIOL_001 (Y94Y, chain C/F/I/M/P/S/T/W, )
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/M/P/S/T/W
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,K: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
K:196-204
L:196-204
O:196-204
R:196-204
V:196-204
[
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]
Exons
(0, 0)
Info
All Exons
View:
Select:
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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.
SCOP Domains
(3, 24)
Info
All SCOP Domains
1a: SCOP_d1rcxb2 (B:9-147)
1b: SCOP_d1rcxe2 (E:9-147)
1c: SCOP_d1rcxh2 (H:9-147)
1d: SCOP_d1rcxk2 (K:9-147)
1e: SCOP_d1rcxl2 (L:9-147)
1f: SCOP_d1rcxo2 (O:9-147)
1g: SCOP_d1rcxr2 (R:9-147)
1h: SCOP_d1rcxv2 (V:9-147)
2a: SCOP_d1rcxc_ (C:)
2b: SCOP_d1rcxf_ (F:)
2c: SCOP_d1rcxi_ (I:)
2d: SCOP_d1rcxm_ (M:)
2e: SCOP_d1rcxp_ (P:)
2f: SCOP_d1rcxs_ (S:)
2g: SCOP_d1rcxt_ (T:)
2h: SCOP_d1rcxw_ (W:)
3a: SCOP_d1rcxb1 (B:148-475)
3b: SCOP_d1rcxe1 (E:148-475)
3c: SCOP_d1rcxh1 (H:148-475)
3d: SCOP_d1rcxk1 (K:148-475)
3e: SCOP_d1rcxl1 (L:148-475)
3f: SCOP_d1rcxo1 (O:148-475)
3g: SCOP_d1rcxr1 (R:148-475)
3h: SCOP_d1rcxv1 (V:148-475)
View:
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Classes
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)
(
)
Folds
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)
(
)
Superfamilies
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)
(
)
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
d1rcxb2
B:9-147
1b
d1rcxe2
E:9-147
1c
d1rcxh2
H:9-147
1d
d1rcxk2
K:9-147
1e
d1rcxl2
L:9-147
1f
d1rcxo2
O:9-147
1g
d1rcxr2
R:9-147
1h
d1rcxv2
V: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
d1rcxc_
C:
2b
d1rcxf_
F:
2c
d1rcxi_
I:
2d
d1rcxm_
M:
2e
d1rcxp_
P:
2f
d1rcxs_
S:
2g
d1rcxt_
T:
2h
d1rcxw_
W:
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
d1rcxb1
B:148-475
3b
d1rcxe1
E:148-475
3c
d1rcxh1
H:148-475
3d
d1rcxk1
K:148-475
3e
d1rcxl1
L:148-475
3f
d1rcxo1
O:148-475
3g
d1rcxr1
R:148-475
3h
d1rcxv1
V:148-475
[
close SCOP info
]
CATH Domains
(3, 24)
Info
all CATH domains
1a: CATH_1rcxB01 (B:22-148)
1b: CATH_1rcxE01 (E:22-148)
1c: CATH_1rcxH01 (H:22-148)
1d: CATH_1rcxK01 (K:22-148)
1e: CATH_1rcxL01 (L:22-148)
1f: CATH_1rcxO01 (O:22-148)
1g: CATH_1rcxR01 (R:22-148)
1h: CATH_1rcxV01 (V:22-148)
2a: CATH_1rcxC00 (C:1-123)
2b: CATH_1rcxF00 (F:1-123)
2c: CATH_1rcxI00 (I:1-123)
2d: CATH_1rcxM00 (M:1-123)
2e: CATH_1rcxP00 (P:1-123)
2f: CATH_1rcxS00 (S:1-123)
2g: CATH_1rcxT00 (T:1-123)
2h: CATH_1rcxW00 (W:1-123)
3a: CATH_1rcxB02 (B:149-462)
3b: CATH_1rcxE02 (E:149-462)
3c: CATH_1rcxH02 (H:149-462)
3d: CATH_1rcxK02 (K:149-462)
3e: CATH_1rcxL02 (L:149-462)
3f: CATH_1rcxO02 (O:149-462)
3g: CATH_1rcxR02 (R:149-462)
3h: CATH_1rcxV02 (V:149-462)
View:
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)
(
)
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
1rcxB01
B:22-148
1b
1rcxE01
E:22-148
1c
1rcxH01
H:22-148
1d
1rcxK01
K:22-148
1e
1rcxL01
L:22-148
1f
1rcxO01
O:22-148
1g
1rcxR01
R:22-148
1h
1rcxV01
V: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
1rcxC00
C:1-123
2b
1rcxF00
F:1-123
2c
1rcxI00
I:1-123
2d
1rcxM00
M:1-123
2e
1rcxP00
P:1-123
2f
1rcxS00
S:1-123
2g
1rcxT00
T:1-123
2h
1rcxW00
W:1-123
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Rubisco
(49)
Spinach (Spinacia oleracea)
(10)
3a
1rcxB02
B:149-462
3b
1rcxE02
E:149-462
3c
1rcxH02
H:149-462
3d
1rcxK02
K:149-462
3e
1rcxL02
L:149-462
3f
1rcxO02
O:149-462
3g
1rcxR02
R:149-462
3h
1rcxV02
V:149-462
[
close CATH info
]
Pfam Domains
(3, 24)
Info
all PFAM domains
1a: PFAM_RuBisCO_large_1rcxV01 (V:154-462)
1b: PFAM_RuBisCO_large_1rcxV02 (V:154-462)
1c: PFAM_RuBisCO_large_1rcxV03 (V:154-462)
1d: PFAM_RuBisCO_large_1rcxV04 (V:154-462)
1e: PFAM_RuBisCO_large_1rcxV05 (V:154-462)
1f: PFAM_RuBisCO_large_1rcxV06 (V:154-462)
1g: PFAM_RuBisCO_large_1rcxV07 (V:154-462)
1h: PFAM_RuBisCO_large_1rcxV08 (V:154-462)
2a: PFAM_RuBisCO_large_N_1rcxV09 (V:21-146)
2b: PFAM_RuBisCO_large_N_1rcxV10 (V:21-146)
2c: PFAM_RuBisCO_large_N_1rcxV11 (V:21-146)
2d: PFAM_RuBisCO_large_N_1rcxV12 (V:21-146)
2e: PFAM_RuBisCO_large_N_1rcxV13 (V:21-146)
2f: PFAM_RuBisCO_large_N_1rcxV14 (V:21-146)
2g: PFAM_RuBisCO_large_N_1rcxV15 (V:21-146)
2h: PFAM_RuBisCO_large_N_1rcxV16 (V:21-146)
3a: PFAM_RuBisCO_small_1rcxW01 (W:11-121)
3b: PFAM_RuBisCO_small_1rcxW02 (W:11-121)
3c: PFAM_RuBisCO_small_1rcxW03 (W:11-121)
3d: PFAM_RuBisCO_small_1rcxW04 (W:11-121)
3e: PFAM_RuBisCO_small_1rcxW05 (W:11-121)
3f: PFAM_RuBisCO_small_1rcxW06 (W:11-121)
3g: PFAM_RuBisCO_small_1rcxW07 (W:11-121)
3h: PFAM_RuBisCO_small_1rcxW08 (W:11-121)
View:
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Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: RuBisCO_large]
(36)
Family
:
RuBisCO_large
(36)
Spinacia oleracea (Spinach)
(6)
1a
RuBisCO_large-1rcxV01
V:154-462
1b
RuBisCO_large-1rcxV02
V:154-462
1c
RuBisCO_large-1rcxV03
V:154-462
1d
RuBisCO_large-1rcxV04
V:154-462
1e
RuBisCO_large-1rcxV05
V:154-462
1f
RuBisCO_large-1rcxV06
V:154-462
1g
RuBisCO_large-1rcxV07
V:154-462
1h
RuBisCO_large-1rcxV08
V:154-462
Clan
:
no clan defined [family: RuBisCO_large_N]
(27)
Family
:
RuBisCO_large_N
(27)
Spinacia oleracea (Spinach)
(6)
2a
RuBisCO_large_N-1rcxV09
V:21-146
2b
RuBisCO_large_N-1rcxV10
V:21-146
2c
RuBisCO_large_N-1rcxV11
V:21-146
2d
RuBisCO_large_N-1rcxV12
V:21-146
2e
RuBisCO_large_N-1rcxV13
V:21-146
2f
RuBisCO_large_N-1rcxV14
V:21-146
2g
RuBisCO_large_N-1rcxV15
V:21-146
2h
RuBisCO_large_N-1rcxV16
V:21-146
Clan
:
no clan defined [family: RuBisCO_small]
(23)
Family
:
RuBisCO_small
(23)
Spinacia oleracea (Spinach)
(6)
3a
RuBisCO_small-1rcxW01
W:11-121
3b
RuBisCO_small-1rcxW02
W:11-121
3c
RuBisCO_small-1rcxW03
W:11-121
3d
RuBisCO_small-1rcxW04
W:11-121
3e
RuBisCO_small-1rcxW05
W:11-121
3f
RuBisCO_small-1rcxW06
W:11-121
3g
RuBisCO_small-1rcxW07
W:11-121
3h
RuBisCO_small-1rcxW08
W:11-121
[
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]
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