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3WQP
Asym. Unit
Info
Asym.Unit (1.5 MB)
Biol.Unit 1, α-C (1.4 MB)
Biol.Unit 1 (1.4 MB)
Biol.Unit 2, α-C (1.4 MB)
Biol.Unit 2 (1.4 MB)
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(1)
Title
:
CRYSTAL STRUCTURE OF RUBISCO T289D MUTANT FROM THERMOCOCCUS KODAKARENSIS
Authors
:
M. Fujihashi, Y. Nishitani, T. Kiriyama, K. Miki
Date
:
29 Jan 14 (Deposition) - 04 Feb 15 (Release) - 04 Feb 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.25
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J
Biol. Unit 1: A,B,C,D,E (2x)
Biol. Unit 2: F,G,H,I,J (2x)
Keywords
:
Decamer, Protein-Ligand Complex, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Kiriyama, M. Fujihashi, Y. Nishitani, R. Aono, T. Sato, T. Takai, K. Tagashira, W. Fukuda, H. Atomi, T. Imanaka, K. Miki
Mutation Design Of Thermophilic Rubisco Based On The Three-Dimensional Structure Enhances Its Activity At Ambien Temperature
To Be Published
[
close entry info
]
Hetero Components
(4, 40)
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)
1e: 2-CARBOXYARABINITOL-1,5-DIPHOSPHAT... (CAPe)
1f: 2-CARBOXYARABINITOL-1,5-DIPHOSPHAT... (CAPf)
1g: 2-CARBOXYARABINITOL-1,5-DIPHOSPHAT... (CAPg)
1h: 2-CARBOXYARABINITOL-1,5-DIPHOSPHAT... (CAPh)
1i: 2-CARBOXYARABINITOL-1,5-DIPHOSPHAT... (CAPi)
1j: 2-CARBOXYARABINITOL-1,5-DIPHOSPHAT... (CAPj)
2a: 1,2-ETHANEDIOL (EDOa)
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)
3a: LYSINE NZ-CARBOXYLIC ACID (KCXa)
3b: LYSINE NZ-CARBOXYLIC ACID (KCXb)
3c: LYSINE NZ-CARBOXYLIC ACID (KCXc)
3d: LYSINE NZ-CARBOXYLIC ACID (KCXd)
3e: LYSINE NZ-CARBOXYLIC ACID (KCXe)
3f: LYSINE NZ-CARBOXYLIC ACID (KCXf)
3g: LYSINE NZ-CARBOXYLIC ACID (KCXg)
3h: LYSINE NZ-CARBOXYLIC ACID (KCXh)
3i: LYSINE NZ-CARBOXYLIC ACID (KCXi)
3j: LYSINE NZ-CARBOXYLIC ACID (KCXj)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
4c: MAGNESIUM ION (MGc)
4d: MAGNESIUM ION (MGd)
4e: MAGNESIUM ION (MGe)
4f: MAGNESIUM ION (MGf)
4g: MAGNESIUM ION (MGg)
4h: MAGNESIUM ION (MGh)
4i: MAGNESIUM ION (MGi)
4j: MAGNESIUM ION (MGj)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CAP
10
Ligand/Ion
2-CARBOXYARABINITOL-1,5-DIPHOSPHATE
2
EDO
10
Ligand/Ion
1,2-ETHANEDIOL
3
KCX
10
Mod. Amino Acid
LYSINE NZ-CARBOXYLIC ACID
4
MG
10
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(30, 30)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
KCX A:189 , ASP A:191 , GLU A:192 , CAP A:502
BINDING SITE FOR RESIDUE MG A 501
02
AC2
SOFTWARE
LYS A:163 , LYS A:165 , KCX A:189 , ASP A:191 , GLU A:192 , HIS A:281 , ARG A:282 , HIS A:314 , LYS A:322 , LEU A:323 , SER A:367 , GLY A:368 , GLY A:369 , GLN A:389 , GLY A:391 , GLY A:392 , MG A:501 , HOH A:625 , HOH A:641 , HOH A:645 , HOH A:666 , HOH A:703 , HOH A:783 , GLU C:49 , THR C:54 , TRP C:55 , ASN C:111 , HOH C:666 , HOH C:778
BINDING SITE FOR RESIDUE CAP A 502
03
AC3
SOFTWARE
ASP A:214 , LEU A:247 , GLY A:248
BINDING SITE FOR RESIDUE EDO A 503
04
AC4
SOFTWARE
LYS B:165 , KCX B:189 , ASP B:191 , GLU B:192 , CAP B:502
BINDING SITE FOR RESIDUE MG B 501
05
AC5
SOFTWARE
GLU B:49 , THR B:54 , TRP B:55 , ASN B:111 , LYS B:163 , LYS B:165 , KCX B:189 , ASP B:191 , GLU B:192 , HIS B:281 , ARG B:282 , HIS B:314 , LYS B:322 , LEU B:323 , SER B:367 , GLY B:368 , GLY B:369 , GLN B:389 , GLY B:391 , GLY B:392 , MG B:501 , HOH B:638 , HOH B:681 , HOH B:686 , HOH B:725 , HOH B:726 , HOH B:727
BINDING SITE FOR RESIDUE CAP B 502
06
AC6
SOFTWARE
GLU B:97 , ALA B:99 , ASN B:100 , LEU B:101 , GLU B:135 , PHE B:136 , HOH B:667 , HOH B:688 , HOH B:708
BINDING SITE FOR RESIDUE EDO B 503
07
AC7
SOFTWARE
ASN A:111 , LYS C:165 , KCX C:189 , ASP C:191 , GLU C:192 , CAP C:502
BINDING SITE FOR RESIDUE MG C 501
08
AC8
SOFTWARE
GLU A:49 , TRP A:55 , ASN A:111 , HOH A:624 , HOH A:686 , LYS C:163 , LYS C:165 , KCX C:189 , ASP C:191 , GLU C:192 , HIS C:281 , ARG C:282 , HIS C:314 , LYS C:322 , LEU C:323 , SER C:367 , GLY C:368 , GLY C:369 , GLN C:389 , GLY C:391 , GLY C:392 , MG C:501 , HOH C:674 , HOH C:684 , HOH C:685 , HOH C:754 , HOH C:821
BINDING SITE FOR RESIDUE CAP C 502
09
AC9
SOFTWARE
GLU C:97 , ALA C:99 , ASN C:100 , LEU C:101 , GLU C:135 , PHE C:136 , HOH C:665 , HOH C:815
BINDING SITE FOR RESIDUE EDO C 503
10
BC1
SOFTWARE
LYS D:163 , KCX D:189 , ASP D:191 , GLU D:192 , CAP D:502
BINDING SITE FOR RESIDUE MG D 501
11
BC2
SOFTWARE
LYS D:163 , LYS D:165 , KCX D:189 , ASP D:191 , GLU D:192 , HIS D:281 , ARG D:282 , HIS D:314 , LYS D:322 , LEU D:323 , SER D:367 , GLY D:368 , GLY D:369 , GLN D:389 , GLY D:391 , GLY D:392 , MG D:501 , HOH D:611 , HOH D:619 , HOH D:632 , HOH D:650 , HOH D:659 , HOH D:828 , GLU E:49 , THR E:54 , TRP E:55 , ASN E:111 , HOH E:660 , HOH E:727
BINDING SITE FOR RESIDUE CAP D 502
12
BC3
SOFTWARE
GLU D:97 , ALA D:99 , ASN D:100 , LEU D:101 , LEU D:132 , GLU D:135 , PHE D:136 , HOH D:655 , HOH D:835
BINDING SITE FOR RESIDUE EDO D 503
13
BC4
SOFTWARE
ASN D:111 , KCX E:189 , ASP E:191 , GLU E:192 , CAP E:502
BINDING SITE FOR RESIDUE MG E 501
14
BC5
SOFTWARE
TRP D:55 , ASN D:111 , LYS E:163 , LYS E:165 , KCX E:189 , ASP E:191 , GLU E:192 , HIS E:281 , ARG E:282 , HIS E:314 , LYS E:322 , LEU E:323 , SER E:367 , GLY E:368 , GLY E:369 , GLN E:389 , GLY E:391 , GLY E:392 , MG E:501 , HOH E:640 , HOH E:659 , HOH E:688 , HOH E:708 , HOH E:776 , HOH E:781 , HOH E:851 , HOH E:852
BINDING SITE FOR RESIDUE CAP E 502
15
BC6
SOFTWARE
GLU D:238 , TYR D:266 , GLU E:238
BINDING SITE FOR RESIDUE EDO E 503
16
BC7
SOFTWARE
KCX F:189 , ASP F:191 , GLU F:192 , CAP F:502
BINDING SITE FOR RESIDUE MG F 501
17
BC8
SOFTWARE
LYS F:163 , LYS F:165 , KCX F:189 , ASP F:191 , GLU F:192 , HIS F:281 , ARG F:282 , HIS F:314 , LYS F:322 , LEU F:323 , SER F:367 , GLY F:368 , GLY F:369 , GLN F:389 , GLY F:391 , GLY F:392 , MG F:501 , HOH F:652 , HOH F:663 , HOH F:666 , HOH F:692 , HOH F:770 , GLU H:49 , THR H:54 , TRP H:55 , ASN H:111 , HOH H:721
BINDING SITE FOR RESIDUE CAP F 502
18
BC9
SOFTWARE
LYS G:165 , KCX G:189 , ASP G:191 , GLU G:192 , CAP G:502
BINDING SITE FOR RESIDUE MG G 501
19
CC1
SOFTWARE
GLU G:49 , TRP G:55 , ASN G:111 , LYS G:163 , LYS G:165 , KCX G:189 , ASP G:191 , GLU G:192 , HIS G:281 , ARG G:282 , HIS G:314 , LYS G:322 , LEU G:323 , SER G:367 , GLY G:368 , GLY G:369 , GLN G:389 , GLY G:391 , GLY G:392 , MG G:501 , HOH G:622 , HOH G:634 , HOH G:668 , HOH G:683 , HOH G:699 , HOH G:732 , HOH G:733
BINDING SITE FOR RESIDUE CAP G 502
20
CC2
SOFTWARE
LYS H:165 , KCX H:189 , ASP H:191 , GLU H:192 , CAP H:502
BINDING SITE FOR RESIDUE MG H 501
21
CC3
SOFTWARE
GLU F:49 , TRP F:55 , ASN F:111 , LYS H:163 , LYS H:165 , KCX H:189 , ASP H:191 , GLU H:192 , HIS H:281 , ARG H:282 , HIS H:314 , LYS H:322 , LEU H:323 , SER H:367 , GLY H:368 , GLY H:369 , GLN H:389 , GLY H:391 , GLY H:392 , MG H:501 , HOH H:646 , HOH H:664 , HOH H:699 , HOH H:748 , HOH H:782 , HOH H:783
BINDING SITE FOR RESIDUE CAP H 502
22
CC4
SOFTWARE
GLU H:97 , ALA H:99 , ASN H:100 , LEU H:101 , GLU H:135 , PHE H:136 , HOH H:651 , HOH H:753
BINDING SITE FOR RESIDUE EDO H 503
23
CC5
SOFTWARE
GLU F:238 , GLU H:238 , TYR H:266
BINDING SITE FOR RESIDUE EDO H 504
24
CC6
SOFTWARE
LYS I:163 , LYS I:165 , KCX I:189 , ASP I:191 , GLU I:192 , CAP I:502
BINDING SITE FOR RESIDUE MG I 501
25
CC7
SOFTWARE
LYS I:163 , LYS I:165 , KCX I:189 , ASP I:191 , GLU I:192 , HIS I:281 , ARG I:282 , HIS I:314 , LYS I:322 , LEU I:323 , SER I:367 , GLY I:368 , GLY I:369 , GLN I:389 , GLY I:391 , GLY I:392 , MG I:501 , HOH I:617 , HOH I:621 , HOH I:638 , HOH I:672 , HOH I:673 , HOH I:676 , HOH I:694 , HOH I:759 , GLU J:49 , THR J:54 , TRP J:55 , ASN J:111
BINDING SITE FOR RESIDUE CAP I 502
26
CC8
SOFTWARE
GLU I:97 , ALA I:99 , ASN I:100 , LEU I:101 , GLU I:135 , PHE I:136 , HOH I:656 , HOH I:811
BINDING SITE FOR RESIDUE EDO I 503
27
CC9
SOFTWARE
GLU I:238 , TYR I:266 , GLU J:238 , TYR J:266
BINDING SITE FOR RESIDUE EDO I 504
28
DC1
SOFTWARE
KCX J:189 , ASP J:191 , GLU J:192 , CAP J:502
BINDING SITE FOR RESIDUE MG J 501
29
DC2
SOFTWARE
GLU I:49 , TRP I:55 , ASN I:111 , HOH I:631 , HOH I:706 , LYS J:163 , LYS J:165 , KCX J:189 , ASP J:191 , GLU J:192 , HIS J:281 , ARG J:282 , HIS J:314 , LYS J:322 , LEU J:323 , SER J:367 , GLY J:368 , GLY J:369 , GLN J:389 , GLY J:391 , GLY J:392 , MG J:501 , HOH J:679 , HOH J:706 , HOH J:713 , HOH J:718 , HOH J:804 , HOH J:835 , HOH J:854
BINDING SITE FOR RESIDUE CAP J 502
30
DC3
SOFTWARE
GLU J:97 , ALA J:99 , ASN J:100 , LEU J:132 , GLU J:135 , PHE J:136
BINDING SITE FOR RESIDUE EDO J 503
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are not available)
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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