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1J2B
Asym. Unit
Info
Asym.Unit (261 KB)
Biol.Unit 1 (254 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF ARCHAEOSINE TRNA-GUANINE TRANSGLYCOSYLASE COMPLEXED WITH LAMBDA-FORM TRNA(VAL)
Authors
:
R. Ishitani, O. Nureki, N. Nameki, N. Okada, S. Nishimura, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date
:
29 Dec 02 (Deposition) - 27 May 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.30
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Transferase, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Transferase/Rna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. Ishitani, O. Nureki, N. Nameki, N. Okada, S. Nishimura, S. Yokoyama
Alternative Tertiary Structure Of Trna For Recognition By A Posttranscriptional Modification Enzyme
Cell(Cambridge, Mass. ) V. 113 383 2003
(for further references see the
PDB file header
)
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Hetero Components
(2, 6)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
1c: MAGNESIUM ION (MGc)
1d: MAGNESIUM ION (MGd)
2a: ZINC ION (ZNa)
2b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MG
4
Ligand/Ion
MAGNESIUM ION
2
ZN
2
Ligand/Ion
ZINC ION
[
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Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
TYR A:262 , CYS A:279 , CYS A:281 , CYS A:284 , HIS A:307
BINDING SITE FOR RESIDUE ZN A 600
2
AC2
SOFTWARE
ALA A:528 , VAL A:531 , MET A:566 , ILE A:567 , PHE A:569
BINDING SITE FOR RESIDUE MG A 601
3
AC3
SOFTWARE
ARG B:573
BINDING SITE FOR RESIDUE MG B 602
4
AC4
SOFTWARE
CYS B:279 , CYS B:281 , CYS B:284 , HIS B:307
BINDING SITE FOR RESIDUE ZN B 600
5
AC5
SOFTWARE
ALA B:528 , LYS B:529 , VAL B:531 , MET B:566 , ILE B:567 , PHE B:569 , GLN B:570
BINDING SITE FOR RESIDUE MG B 1601
6
AC6
SOFTWARE
ARG A:573
BINDING SITE FOR RESIDUE MG C 1602
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: PUA (A:507-582,B:507-582)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PUA
PS50890
PUA domain profile.
ATGT_PYRHO
507-582
2
A:507-582
B:507-582
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Exons
(0, 0)
Info
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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, 6)
Info
All SCOP Domains
1a: SCOP_d1j2ba1 (A:506-582)
1b: SCOP_d1j2bb1 (B:506-582)
2a: SCOP_d1j2ba3 (A:361-505)
2b: SCOP_d1j2bb3 (B:361-505)
3a: SCOP_d1j2ba2 (A:7-360)
3b: SCOP_d1j2bb2 (B:7-360)
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)
(
)
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)
(
)
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(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
PUA domain-like
(96)
Superfamily
:
PUA domain-like
(96)
Family
:
PUA domain
(22)
Protein domain
:
Archaeosine tRNA-guanine transglycosylase, C3 domain
(4)
Pyrococcus horikoshii [TaxId: 53953]
(4)
1a
d1j2ba1
A:506-582
1b
d1j2bb1
B:506-582
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Cystatin-like
(403)
Superfamily
:
Pre-PUA domain
(11)
Family
:
Archaeosine tRNA-guanine transglycosylase, C2 domain
(4)
Protein domain
:
Archaeosine tRNA-guanine transglycosylase, C2 domain
(4)
Pyrococcus horikoshii [TaxId: 53953]
(4)
2a
d1j2ba3
A:361-505
2b
d1j2bb3
B:361-505
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
TIM beta/alpha-barrel
(3956)
Superfamily
:
tRNA-guanine transglycosylase
(91)
Family
:
tRNA-guanine transglycosylase
(91)
Protein domain
:
Archaeosine tRNA-guanine transglycosylase, N-terminal domain
(4)
Pyrococcus horikoshii [TaxId: 53953]
(4)
3a
d1j2ba2
A:7-360
3b
d1j2bb2
B:7-360
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CATH Domains
(4, 8)
Info
all CATH domains
1a: CATH_1j2bA01 (A:7-360)
1b: CATH_1j2bB01 (B:7-360)
2a: CATH_1j2bA02 (A:361-430)
2b: CATH_1j2bB02 (B:361-430)
3a: CATH_1j2bA03 (A:431-504)
3b: CATH_1j2bB03 (B:431-504)
4a: CATH_1j2bA04 (A:505-582)
4b: CATH_1j2bB04 (B:505-582)
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Classes
(
)
(
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(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Barrel
(2994)
Topology
:
TIM Barrel
(2806)
Homologous Superfamily
:
tRNA-guanine (tRNA-G) transglycosylase
(61)
[unclassified]
(3)
1a
1j2bA01
A:7-360
1b
1j2bB01
B:7-360
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 2
(4)
Homologous Superfamily
:
[code=3.90.1020.10, no name defined]
(4)
[unclassified]
(1)
2a
1j2bA02
A:361-430
2b
1j2bB02
B:361-430
Architecture
:
Roll
(3276)
Topology
:
Nuclear Transport Factor 2; Chain: A,
(517)
Homologous Superfamily
:
[code=3.10.450.90, no name defined]
(5)
[unclassified]
(1)
3a
1j2bA03
A:431-504
3b
1j2bB03
B:431-504
Class
:
Mainly Beta
(13760)
Architecture
:
Roll
(1513)
Topology
:
Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4
(16)
Homologous Superfamily
:
[code=2.30.130.10, no name defined]
(14)
[unclassified]
(3)
4a
1j2bA04
A:505-582
4b
1j2bB04
B:505-582
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Chain D
Asymmetric Unit 1
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Asym.Unit (261 KB)
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