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1GK8
Asym. Unit
Info
Asym.Unit (441 KB)
Biol.Unit 1 (853 KB)
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(1)
Title
:
RUBISCO FROM CHLAMYDOMONAS REINHARDTII
Authors
:
T. C. Taylor, R. J. Spreitzer, I. Andersson
Date
:
09 Aug 01 (Deposition) - 24 Oct 01 (Release) - 15 Apr 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.40
Chains
:
Asym. Unit : A,C,E,G,I,K,M,O
Biol. Unit 1: A,C,E,G,I,K,M,O (2x)
Keywords
:
Lyase, Rubisco, Photosynthesis
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. C. Taylor, A. Backlund, K. Bjorhall, R. J. Spreitzer, I. Andersson
First Crystal Structure Of Rubisco From A Green Alga, Chlamydomonas Reinhardtii.
J. Biol. Chem. V. 276 48159 2001
[
close entry info
]
Hetero Components
(7, 65)
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: 1,2-ETHANEDIOL (EDOa)
2aa: 1,2-ETHANEDIOL (EDOaa)
2ab: 1,2-ETHANEDIOL (EDOab)
2ac: 1,2-ETHANEDIOL (EDOac)
2ad: 1,2-ETHANEDIOL (EDOad)
2ae: 1,2-ETHANEDIOL (EDOae)
2af: 1,2-ETHANEDIOL (EDOaf)
2ag: 1,2-ETHANEDIOL (EDOag)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
2f: 1,2-ETHANEDIOL (EDOf)
2g: 1,2-ETHANEDIOL (EDOg)
2h: 1,2-ETHANEDIOL (EDOh)
2i: 1,2-ETHANEDIOL (EDOi)
2j: 1,2-ETHANEDIOL (EDOj)
2k: 1,2-ETHANEDIOL (EDOk)
2l: 1,2-ETHANEDIOL (EDOl)
2m: 1,2-ETHANEDIOL (EDOm)
2n: 1,2-ETHANEDIOL (EDOn)
2o: 1,2-ETHANEDIOL (EDOo)
2p: 1,2-ETHANEDIOL (EDOp)
2q: 1,2-ETHANEDIOL (EDOq)
2r: 1,2-ETHANEDIOL (EDOr)
2s: 1,2-ETHANEDIOL (EDOs)
2t: 1,2-ETHANEDIOL (EDOt)
2u: 1,2-ETHANEDIOL (EDOu)
2v: 1,2-ETHANEDIOL (EDOv)
2w: 1,2-ETHANEDIOL (EDOw)
2x: 1,2-ETHANEDIOL (EDOx)
2y: 1,2-ETHANEDIOL (EDOy)
2z: 1,2-ETHANEDIOL (EDOz)
3a: 4-HYDROXYPROLINE (HYPa)
3b: 4-HYDROXYPROLINE (HYPb)
3c: 4-HYDROXYPROLINE (HYPc)
3d: 4-HYDROXYPROLINE (HYPd)
3e: 4-HYDROXYPROLINE (HYPe)
3f: 4-HYDROXYPROLINE (HYPf)
3g: 4-HYDROXYPROLINE (HYPg)
3h: 4-HYDROXYPROLINE (HYPh)
4a: LYSINE NZ-CARBOXYLIC ACID (KCXa)
4b: LYSINE NZ-CARBOXYLIC ACID (KCXb)
4c: LYSINE NZ-CARBOXYLIC ACID (KCXc)
4d: LYSINE NZ-CARBOXYLIC ACID (KCXd)
5a: MAGNESIUM ION (MGa)
5b: MAGNESIUM ION (MGb)
5c: MAGNESIUM ION (MGc)
5d: MAGNESIUM ION (MGd)
6a: N-METHYL METHIONINE (MMEa)
6b: N-METHYL METHIONINE (MMEb)
6c: N-METHYL METHIONINE (MMEc)
6d: N-METHYL METHIONINE (MMEd)
7a: S-METHYLCYSTEINE (SMCa)
7b: S-METHYLCYSTEINE (SMCb)
7c: S-METHYLCYSTEINE (SMCc)
7d: S-METHYLCYSTEINE (SMCd)
7e: S-METHYLCYSTEINE (SMCe)
7f: S-METHYLCYSTEINE (SMCf)
7g: S-METHYLCYSTEINE (SMCg)
7h: S-METHYLCYSTEINE (SMCh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CAP
4
Ligand/Ion
2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
2
EDO
33
Ligand/Ion
1,2-ETHANEDIOL
3
HYP
8
Mod. Amino Acid
4-HYDROXYPROLINE
4
KCX
4
Mod. Amino Acid
LYSINE NZ-CARBOXYLIC ACID
5
MG
4
Ligand/Ion
MAGNESIUM ION
6
MME
4
Mod. Amino Acid
N-METHYL METHIONINE
7
SMC
8
Mod. Amino Acid
S-METHYLCYSTEINE
[
close Hetero Component info
]
Sites
(41, 41)
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: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LYS A:177 , KCX A:201 , ASP A:203 , GLU A:204 , CAP A:1477
BINDING SITE FOR RESIDUE MG A1476
02
AC2
SOFTWARE
LYS C:177 , KCX C:201 , ASP C:203 , GLU C:204 , CAP C:1477
BINDING SITE FOR RESIDUE MG C1476
03
AC3
SOFTWARE
LYS E:177 , KCX E:201 , ASP E:203 , GLU E:204 , CAP E:1477
BINDING SITE FOR RESIDUE MG E1476
04
AC4
SOFTWARE
KCX G:201 , ASP G:203 , GLU G:204 , CAP G:1477
BINDING SITE FOR RESIDUE MG G1476
05
AC5
SOFTWARE
GLU A:60 , THR A:65 , TRP A:66 , ASN A:123 , 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:1476 , HOH A:2153 , HOH A:2443 , HOH A:2444 , HOH A:2445 , HOH A:2446 , HOH A:2447 , HOH A:2448
BINDING SITE FOR RESIDUE CAP A1477
06
AC6
SOFTWARE
TYR A:24 , GLY A:64 , THR A:68 , VAL A:69 , ASP A:72 , LEU A:77 , HOH A:2449 , HOH A:2450 , HOH A:2451
BINDING SITE FOR RESIDUE EDO A1478
07
AC7
SOFTWARE
VAL A:17 , LYS A:18 , THR A:65 , TRP A:66 , THR A:67 , THR A:68 , HOH A:2451 , HOH A:2452
BINDING SITE FOR RESIDUE EDO A1479
08
AC8
SOFTWARE
GLU A:52 , HOH A:2453 , HOH A:2454 , HOH A:2455
BINDING SITE FOR RESIDUE EDO A1480
09
AC9
SOFTWARE
GLY A:47 , VAL A:48 , PRO A:49 , GLU A:52 , HOH A:2022 , HOH A:2455 , HOH A:2456 , HOH A:2457
BINDING SITE FOR RESIDUE EDO A1481
10
BC1
SOFTWARE
LYS A:466 , PHE A:467 , GLU A:468 , PHE A:469 , HOH A:2453 , HOH A:2458
BINDING SITE FOR RESIDUE EDO A1482
11
BC2
SOFTWARE
HIS A:298 , PHE A:311 , GLU A:336 , ASP A:473 , HOH A:2286 , HOH A:2310 , HOH A:2459 , HOH A:2460
BINDING SITE FOR RESIDUE EDO A1483
12
BC3
SOFTWARE
LEU A:270 , HOH A:2461
BINDING SITE FOR RESIDUE EDO A1484
13
BC4
SOFTWARE
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:1476 , HOH C:2453 , HOH C:2454 , HOH C:2455 , HOH C:2456 , HOH C:2457 , HOH C:2458 , GLU G:60 , THR G:65 , TRP G:66 , ASN G:123 , HOH G:2174
BINDING SITE FOR RESIDUE CAP C1477
14
BC5
SOFTWARE
TYR C:24 , GLY C:64 , THR C:68 , VAL C:69 , ASP C:72 , LEU C:77 , EDO C:1479 , HOH C:2459 , HOH C:2460 , HOH C:2461
BINDING SITE FOR RESIDUE EDO C1478
15
BC6
SOFTWARE
GLY C:16 , VAL C:17 , LYS C:18 , THR C:65 , TRP C:66 , THR C:67 , THR C:68 , EDO C:1478 , HOH C:2043 , HOH C:2461
BINDING SITE FOR RESIDUE EDO C1479
16
BC7
SOFTWARE
GLU C:52 , HOH C:2462 , HOH C:2463
BINDING SITE FOR RESIDUE EDO C1480
17
BC8
SOFTWARE
LYS C:466 , PHE C:467 , GLU C:468 , PHE C:469 , HOH C:2464 , HOH G:2470
BINDING SITE FOR RESIDUE EDO C1481
18
BC9
SOFTWARE
HIS C:298 , PHE C:311 , GLU C:336 , ASP C:473 , HOH C:2286 , HOH C:2309 , HOH C:2465 , HOH C:2466
BINDING SITE FOR RESIDUE EDO C1482
19
CC1
SOFTWARE
GLU E:60 , THR E:65 , TRP E:66 , ASN E:123 , 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:1476 , HOH E:2161 , HOH E:2469 , HOH E:2470 , HOH E:2471 , HOH E:2472 , HOH E:2473 , HOH E:2474
BINDING SITE FOR RESIDUE CAP E1477
20
CC2
SOFTWARE
TYR E:24 , GLY E:64 , THR E:68 , VAL E:69 , ASP E:72 , LEU E:77 , HOH E:2475 , HOH E:2476 , HOH E:2478
BINDING SITE FOR RESIDUE EDO E1478
21
CC3
SOFTWARE
VAL E:17 , LYS E:18 , THR E:65 , TRP E:66 , THR E:67 , THR E:68 , HOH E:2477 , HOH E:2478
BINDING SITE FOR RESIDUE EDO E1479
22
CC4
SOFTWARE
GLU E:52 , EDO E:1481 , HOH E:2479 , HOH E:2480 , HOH E:2483
BINDING SITE FOR RESIDUE EDO E1480
23
CC5
SOFTWARE
GLY E:47 , VAL E:48 , PRO E:49 , GLU E:52 , EDO E:1480 , HOH E:2018 , HOH E:2481 , HOH E:2482 , HOH E:2483
BINDING SITE FOR RESIDUE EDO E1481
24
CC6
SOFTWARE
LYS E:466 , PHE E:467 , GLU E:468 , PHE E:469 , HOH E:2480 , HOH E:2484
BINDING SITE FOR RESIDUE EDO E1482
25
CC7
SOFTWARE
HIS E:298 , PHE E:311 , GLU E:336 , ASP E:473 , HOH E:2301 , HOH E:2325 , HOH E:2485 , HOH E:2486
BINDING SITE FOR RESIDUE EDO E1483
26
CC8
SOFTWARE
LEU E:270 , HOH E:2487
BINDING SITE FOR RESIDUE EDO E1484
27
CC9
SOFTWARE
GLU C:60 , THR C:65 , TRP C:66 , ASN C:123 , HOH C:2150 , 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:1476 , HOH G:2458 , HOH G:2459 , HOH G:2460 , HOH G:2461 , HOH G:2462 , HOH G:2463
BINDING SITE FOR RESIDUE CAP G1477
28
DC1
SOFTWARE
TYR G:24 , GLY G:64 , THR G:68 , VAL G:69 , ASP G:72 , LEU G:77 , HOH G:2464 , HOH G:2465 , HOH G:2466
BINDING SITE FOR RESIDUE EDO G1478
29
DC2
SOFTWARE
VAL G:17 , LYS G:18 , THR G:65 , TRP G:66 , THR G:67 , THR G:68 , HOH G:2466 , HOH G:2467
BINDING SITE FOR RESIDUE EDO G1479
30
DC3
SOFTWARE
GLU G:52 , HOH G:2468 , HOH G:2470
BINDING SITE FOR RESIDUE EDO G1480
31
DC4
SOFTWARE
HOH C:2463 , GLU G:464 , LYS G:466 , PHE G:467 , GLU G:468 , PHE G:469 , HOH G:2442
BINDING SITE FOR RESIDUE EDO G1481
32
DC5
SOFTWARE
HIS G:298 , PHE G:311 , GLU G:336 , ASP G:473 , HOH G:2300 , HOH G:2326 , HOH G:2471 , HOH G:2472
BINDING SITE FOR RESIDUE EDO G1482
33
DC6
SOFTWARE
LEU C:270 , LEU G:270 , HOH G:2473 , HOH G:2474
BINDING SITE FOR RESIDUE EDO G1483
34
DC7
SOFTWARE
TYR C:226 , HOH C:2237 , LYS I:49 , GLU I:55 , HOH I:2104
BINDING SITE FOR RESIDUE EDO I1127
35
DC8
SOFTWARE
GLY I:37 , TRP I:38 , ILE I:39 , PHE I:81 , GLY I:82 , CYS I:83 , HOH I:2157
BINDING SITE FOR RESIDUE EDO I1128
36
DC9
SOFTWARE
TYR E:226 , HOH E:2251 , LYS K:49 , GLU K:55 , HOH K:2110 , HOH K:2166
BINDING SITE FOR RESIDUE EDO K1127
37
EC1
SOFTWARE
GLY K:37 , TRP K:38 , ILE K:39 , GLY K:82 , CYS K:83 , HOH K:2167 , HOH K:2168
BINDING SITE FOR RESIDUE EDO K1128
38
EC2
SOFTWARE
TYR G:226 , HOH G:2254 , LYS M:49 , GLU M:55 , HOH M:2113 , HOH M:2168
BINDING SITE FOR RESIDUE EDO M1127
39
EC3
SOFTWARE
GLY M:37 , TRP M:38 , ILE M:39 , GLY M:82 , CYS M:83 , ARG M:84 , HOH M:2170
BINDING SITE FOR RESIDUE EDO M1128
40
EC4
SOFTWARE
TYR A:226 , ALA A:230 , HOH A:2237 , LYS O:49 , GLU O:55 , HOH O:2113 , HOH O:2171
BINDING SITE FOR RESIDUE EDO O1127
41
EC5
SOFTWARE
GLY O:37 , TRP O:38 , ILE O:39 , GLY O:82 , CYS O:83 , HOH O:2172
BINDING SITE FOR RESIDUE EDO O1128
[
close Site info
]
SAPs(SNPs)/Variants
(1, 4)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_RBL_CHLRE_001 (P46P, chain A/C/E/G, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_RBL_CHLRE_001
*
L
46
P
RBL_CHLRE
---
---
A/C/E/G
P
46
P
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
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:
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_CHLRE
196-204
4
A:196-204
C:196-204
E:196-204
G: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.
SCOP Domains
(3, 12)
Info
All SCOP Domains
1a: SCOP_d1gk8a2 (A:7-149)
1b: SCOP_d1gk8c2 (C:7-149)
1c: SCOP_d1gk8e2 (E:11-149)
1d: SCOP_d1gk8g2 (G:9-149)
2a: SCOP_d1gk8i_ (I:)
2b: SCOP_d1gk8k_ (K:)
2c: SCOP_d1gk8m_ (M:)
2d: SCOP_d1gk8o_ (O:)
3a: SCOP_d1gk8a1 (A:150-475)
3b: SCOP_d1gk8c1 (C:150-475)
3c: SCOP_d1gk8e1 (E:150-475)
3d: SCOP_d1gk8g1 (G:150-475)
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)
Green alga (Chlamydomonas reinhardtii) [TaxId: 3055]
(4)
1a
d1gk8a2
A:7-149
1b
d1gk8c2
C:7-149
1c
d1gk8e2
E:11-149
1d
d1gk8g2
G:9-149
Fold
:
RuBisCO, small subunit
(44)
Superfamily
:
RuBisCO, small subunit
(44)
Family
:
RuBisCO, small subunit
(44)
Protein domain
:
Ribulose 1,5-bisphosphate carboxylase-oxygenase
(28)
Green alga (Chlamydomonas reinhardtii) [TaxId: 3055]
(6)
2a
d1gk8i_
I:
2b
d1gk8k_
K:
2c
d1gk8m_
M:
2d
d1gk8o_
O:
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)
Green alga (Chlamydomonas reinhardtii) [TaxId: 3055]
(4)
3a
d1gk8a1
A:150-475
3b
d1gk8c1
C:150-475
3c
d1gk8e1
E:150-475
3d
d1gk8g1
G:150-475
[
close SCOP info
]
CATH Domains
(3, 12)
Info
all CATH domains
1a: CATH_1gk8A01 (A:22-148)
1b: CATH_1gk8C01 (C:22-148)
1c: CATH_1gk8E01 (E:22-148)
1d: CATH_1gk8G01 (G:22-148)
2a: CATH_1gk8I00 (I:2-126)
2b: CATH_1gk8K00 (K:2-126)
2c: CATH_1gk8M00 (M:2-126)
2d: CATH_1gk8O00 (O:2-126)
3a: CATH_1gk8A02 (A:149-462)
3b: CATH_1gk8C02 (C:149-462)
3c: CATH_1gk8E02 (E:149-462)
3d: CATH_1gk8G02 (G:149-462)
View:
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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)
Chlamydomonas reinhardtii. Organism_taxid: 3055.
(5)
1a
1gk8A01
A:22-148
1b
1gk8C01
C:22-148
1c
1gk8E01
E:22-148
1d
1gk8G01
G:22-148
Topology
:
Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase
(42)
Homologous Superfamily
:
[code=3.30.190.10, no name defined]
(35)
Chlamydomonas reinhardtii. Organism_taxid: 3055.
(5)
2a
1gk8I00
I:2-126
2b
1gk8K00
K:2-126
2c
1gk8M00
M:2-126
2d
1gk8O00
O:2-126
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
Rubisco
(49)
Chlamydomonas reinhardtii. Organism_taxid: 3055.
(5)
3a
1gk8A02
A:149-462
3b
1gk8C02
C:149-462
3c
1gk8E02
E:149-462
3d
1gk8G02
G:149-462
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Asymmetric Unit 1
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