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1Q3Q
Asym. Unit
Info
Asym.Unit (341 KB)
Biol.Unit 1, α-C (1.3 MB)
Biol.Unit 1 (1.3 MB)
Biol.Unit 2 (661 KB)
Biol.Unit 3 (662 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE CHAPERONIN FROM THERMOCOCCUS STRAIN KS-1 (TWO-POINT MUTANT COMPLEXED WITH AMP-PNP)
Authors
:
Y. Shomura, T. Yoshida, R. Iizuka, T. Maruyama, M. Yohda, K. Miki
Date
:
31 Jul 03 (Deposition) - 27 Jan 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (4x)
Biol. Unit 2: A,B (4x)
Biol. Unit 3: C,D (4x)
Keywords
:
Chaperone, Chaperonin, Thermosome
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Shomura, T. Yoshida, R. Iizuka, T. Maruyama, M. Yohda, K. Miki
Crystal Structures Of The Group Ii Chaperonin From Thermococcus Strain Ks-1: Steric Hindrance By The Substituted Amino Acid, And Inter-Subunit Rearrangement Between Two Crystal Forms.
J. Mol. Biol. V. 335 1265 2004
(for further references see the
PDB file header
)
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Hetero Components
(2, 8)
Info
All Hetero Components
1a: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPa)
1b: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPb)
1c: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPc)
1d: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPd)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ANP
4
Ligand/Ion
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2
MG
4
Ligand/Ion
MAGNESIUM ION
[
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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:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:95 , ANP A:1528
BINDING SITE FOR RESIDUE MG A 1527
2
AC2
SOFTWARE
ASP B:95 , LYS B:165 , ANP B:2528
BINDING SITE FOR RESIDUE MG B 2527
3
AC3
SOFTWARE
ASP C:95 , LYS C:165 , ANP C:3528
BINDING SITE FOR RESIDUE MG C 3527
4
AC4
SOFTWARE
ASP D:95 , LYS D:165 , ANP D:4528
BINDING SITE FOR RESIDUE MG D 4527
5
AC5
SOFTWARE
THR A:42 , LEU A:43 , GLY A:44 , PRO A:45 , ASP A:64 , CYS A:65 , GLY A:94 , ASP A:95 , GLY A:96 , THR A:97 , THR A:98 , THR A:99 , THR A:160 , THR A:163 , ALA A:410 , GLY A:411 , ILE A:447 , LEU A:451 , ILE A:479 , ILE A:494 , GLU A:496 , HOH A:1008 , HOH A:1009 , HOH A:1106 , MG A:1527
BINDING SITE FOR RESIDUE ANP A 1528
6
AC6
SOFTWARE
THR B:42 , LEU B:43 , GLY B:44 , PRO B:45 , GLY B:94 , ASP B:95 , GLY B:96 , THR B:97 , THR B:98 , THR B:99 , THR B:163 , ALA B:410 , GLY B:411 , LEU B:451 , ILE B:479 , ILE B:494 , GLU B:496 , HOH B:2037 , HOH B:2048 , MG B:2527
BINDING SITE FOR RESIDUE ANP B 2528
7
AC7
SOFTWARE
THR C:42 , LEU C:43 , GLY C:44 , PRO C:45 , ASP C:64 , CYS C:65 , GLY C:94 , ASP C:95 , GLY C:96 , THR C:97 , THR C:98 , THR C:99 , THR C:160 , THR C:163 , ALA C:410 , GLY C:411 , LEU C:451 , ILE C:494 , GLU C:496 , HOH C:3023 , HOH C:3029 , HOH C:3042 , HOH C:3075 , MG C:3527
BINDING SITE FOR RESIDUE ANP C 3528
8
AC8
SOFTWARE
THR D:42 , LEU D:43 , GLY D:44 , PRO D:45 , ASP D:64 , CYS D:65 , GLY D:94 , ASP D:95 , GLY D:96 , THR D:97 , THR D:98 , THR D:99 , ALA D:410 , GLY D:411 , LEU D:451 , ILE D:479 , ILE D:494 , GLU D:496 , HOH D:4026 , HOH D:4076 , HOH D:4110 , MG D:4527
BINDING SITE FOR RESIDUE ANP D 4528
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(3, 12)
Info
All PROSITE Patterns/Profiles
1: TCP1_1 (A:40-52,B:40-52,C:40-52,D:40-52,A:...)
2: TCP1_2 (A:61-77,B:61-77,C:61-77,D:61-77,A:...)
3: TCP1_3 (A:89-97,B:89-97,C:89-97,D:89-97,A:...)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TCP1_1
PS00750
Chaperonins TCP-1 signature 1.
THSA_THEK1
40-52
4
A:40-52
B:40-52
C:40-52
D:40-52
THSA_THEKO
40-52
4
A:40-52
B:40-52
C:40-52
D:40-52
2
TCP1_2
PS00751
Chaperonins TCP-1 signature 2.
THSA_THEK1
61-77
4
A:61-77
B:61-77
C:61-77
D:61-77
THSA_THEKO
61-77
4
A:61-77
B:61-77
C:61-77
D:61-77
3
TCP1_3
PS00995
Chaperonins TCP-1 signature 3.
THSA_THEK1
89-97
4
A:89-97
B:89-97
C:89-97
D:89-97
THSA_THEKO
89-97
4
A:89-97
B:89-97
C:89-97
D:89-97
[
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]
Exons
(0, 0)
Info
All Exons
View:
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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, 12)
Info
All SCOP Domains
1a: SCOP_d1q3qa1 (A:9-145,A:406-526)
1b: SCOP_d1q3qb1 (B:9-145,B:406-526)
1c: SCOP_d1q3qc1 (C:9-145,C:406-526)
1d: SCOP_d1q3qd1 (D:9-145,D:406-526)
2a: SCOP_d1q3qa3 (A:146-216,A:370-405)
2b: SCOP_d1q3qb3 (B:146-216,B:370-405)
2c: SCOP_d1q3qc3 (C:146-216,C:370-405)
2d: SCOP_d1q3qd3 (D:146-216,D:370-405)
3a: SCOP_d1q3qa2 (A:217-369)
3b: SCOP_d1q3qb2 (B:217-369)
3c: SCOP_d1q3qc2 (C:217-369)
3d: SCOP_d1q3qd2 (D:217-369)
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)
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)
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(
)
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)
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)
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
GroEL equatorial domain-like
(23)
Superfamily
:
GroEL equatorial domain-like
(23)
Family
:
Group II chaperonin (CCT, TRIC), ATPase domain
(8)
Protein domain
:
Thermosome, E domain
(8)
Thermococcus sp. ks-1, alpha chain [TaxId: 79679]
(4)
1a
d1q3qa1
A:9-145,A:406-526
1b
d1q3qb1
B:9-145,B:406-526
1c
d1q3qc1
C:9-145,C:406-526
1d
d1q3qd1
D:9-145,D:406-526
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
GroEL-intermediate domain like
(23)
Superfamily
:
GroEL-intermediate domain like
(23)
Family
:
Group II chaperonin (CCT, TRIC), intermediate domain
(8)
Protein domain
:
Thermosome, I domain
(8)
Thermococcus sp. ks-1, alpha chain [TaxId: 79679]
(4)
2a
d1q3qa3
A:146-216,A:370-405
2b
d1q3qb3
B:146-216,B:370-405
2c
d1q3qc3
C:146-216,C:370-405
2d
d1q3qd3
D:146-216,D:370-405
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
The swivelling beta/beta/alpha domain
(136)
Superfamily
:
GroEL apical domain-like
(41)
Family
:
Group II chaperonin (CCT, TRIC), apical domain
(13)
Protein domain
:
Thermosome, A-domain
(13)
Thermococcus sp. ks-1, alpha chain [TaxId: 79679]
(4)
3a
d1q3qa2
A:217-369
3b
d1q3qb2
B:217-369
3c
d1q3qc2
C:217-369
3d
d1q3qd2
D:217-369
[
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]
CATH Domains
(3, 12)
Info
all CATH domains
1a: CATH_1q3qA02 (A:147-217,A:370-405)
1b: CATH_1q3qB02 (B:147-217,B:370-405)
1c: CATH_1q3qC02 (C:147-217,C:370-405)
1d: CATH_1q3qD02 (D:147-217,D:370-405)
2a: CATH_1q3qA03 (A:218-369)
2b: CATH_1q3qB03 (B:218-369)
2c: CATH_1q3qC03 (C:218-369)
2d: CATH_1q3qD03 (D:218-369)
3a: CATH_1q3qA01 (A:9-146,A:406-526)
3b: CATH_1q3qB01 (B:9-146,B:406-526)
3c: CATH_1q3qC01 (C:9-146,C:406-526)
3d: CATH_1q3qD01 (D:9-146,D:406-526)
View:
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)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
GROEL; domain 2
(26)
Homologous Superfamily
:
GROEL, domain 2
(26)
Ks-1 (Thermococcus sp)
(4)
1a
1q3qA02
A:147-217,A:370-405
1b
1q3qB02
B:147-217,B:370-405
1c
1q3qC02
C:147-217,C:370-405
1d
1q3qD02
D:147-217,D:370-405
Architecture
:
3-Layer(bba) Sandwich
(528)
Topology
:
GroEL
(39)
Homologous Superfamily
:
GroEL
(39)
Ks-1 (Thermococcus sp)
(4)
2a
1q3qA03
A:218-369
2b
1q3qB03
B:218-369
2c
1q3qC03
C:218-369
2d
1q3qD03
D:218-369
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
GROEL; domain 1
(26)
Homologous Superfamily
:
GROEL, domain 1
(26)
Ks-1 (Thermococcus sp)
(4)
3a
1q3qA01
A:9-146,A:406-526
3b
1q3qB01
B:9-146,B:406-526
3c
1q3qC01
C:9-146,C:406-526
3d
1q3qD01
D:9-146,D:406-526
[
close CATH info
]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Cpn60_TCP1_1q3qD01 (D:35-526)
1b: PFAM_Cpn60_TCP1_1q3qD02 (D:35-526)
1c: PFAM_Cpn60_TCP1_1q3qD03 (D:35-526)
1d: PFAM_Cpn60_TCP1_1q3qD04 (D:35-526)
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Clans
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)
(
)
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(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: Cpn60_TCP1]
(28)
Family
:
Cpn60_TCP1
(28)
Thermococcus sp. (strain KS-1)
(4)
1a
Cpn60_TCP1-1q3qD01
D:35-526
1b
Cpn60_TCP1-1q3qD02
D:35-526
1c
Cpn60_TCP1-1q3qD03
D:35-526
1d
Cpn60_TCP1-1q3qD04
D:35-526
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Asym.Unit (341 KB)
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