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2ZIN
Biol. Unit 1
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Asym.Unit (55 KB)
Biol.Unit 1 (98 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF PYRROLYSYL-TRNA SYNTHETASE IN COMPLEX WITH BOCLYS AND AN ATP ANALOGUE
Authors
:
T. Yanagisawa, R. Ishii, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date
:
19 Feb 08 (Deposition) - 02 Dec 08 (Release) - 02 Dec 08 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.79
Chains
:
Asym. Unit : A
Biol. Unit 1: A (2x)
Keywords
:
Aminoacyl-Trna Synthetase, Pyrrolysyl-Trna Synthetase, Pyrrolysine, Trna, Atp Analogue, Non-Natural Amino Acid, Unnatural Amino Acid, Atp-Binding, Cytoplasm, Ligase, Nucleotide-Binding, Protein Biosynthesis, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi
(Keyword Search:
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]
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Reference
:
T. Yanagisawa, R. Ishii, R. Fukunaga, T. Kobayashi, K. Sakamoto, S. Yokoyama
Multistep Engineering Of Pyrrolysyl-Trna Synthetase To Genetically Encode N(Varepsilon)-(O-Azidobenzyloxycarbonyl) Lysine For Site-Specific Protein Modification
Chem. Biol. V. 15 1187 2008
(for further references see the
PDB file header
)
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Hetero Components
(3, 6)
Info
All Hetero Components
1a: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPa)
2a: 1,2-ETHANEDIOL (EDOa)
3a: N~6~-(TERT-BUTOXYCARBONYL)-L-LYSIN... (LBYa)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
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No.
Name
Count
Type
Full Name
1
ANP
2
Ligand/Ion
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2
EDO
2
Ligand/Ion
1,2-ETHANEDIOL
3
LBY
2
Ligand/Ion
N~6~-(TERT-BUTOXYCARBONYL)-L-LYSINE
4
MG
-1
Ligand/Ion
MAGNESIUM ION
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Sites
(5, 5)
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1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HOH A:2141 , HOH A:2161 , HOH A:2188 , HOH A:2193
BINDING SITE FOR RESIDUE MG A 701
2
AC2
SOFTWARE
GLU A:396 , SER A:399 , HOH A:2060
BINDING SITE FOR RESIDUE MG A 702
3
AC3
SOFTWARE
ARG A:330 , GLU A:332 , HIS A:338 , LEU A:339 , PHE A:342 , GLU A:396 , LEU A:397 , SER A:398 , SER A:399 , GLY A:421 , GLY A:423 , ARG A:426 , HOH A:2013 , HOH A:2053 , HOH A:2057 , HOH A:2060 , HOH A:2076 , HOH A:2161 , HOH A:2188 , HOH A:2193
BINDING SITE FOR RESIDUE ANP A 501
4
AC4
SOFTWARE
MET A:300 , TYR A:306 , ASN A:346 , CYS A:348 , TRP A:417 , GLY A:419 , ALA A:420 , HOH A:2012
BINDING SITE FOR RESIDUE LBY A 601
5
AC5
SOFTWARE
MET A:276 , TRP A:417 , HOH A:2221
BINDING SITE FOR RESIDUE EDO A 2011
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SAPs(SNPs)/Variants
(0, 0)
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Exons
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SCOP Domains
(0, 0)
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CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_2zinA02 (A:240-454)
2a: CATH_2zinA01 (A:188-239)
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Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
BirA Bifunctional Protein; domain 2
(111)
Homologous Superfamily
:
Bira Bifunctional Protein; Domain 2
(111)
Methanosarcina mazei. Organism_taxid: 2209. Strain: jcm9314.
(5)
1a
2zinA02
A:240-454
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Helix Hairpins
(718)
Homologous Superfamily
:
Helix hairpin bin
(21)
Methanosarcina mazei. Organism_taxid: 2209. Strain: jcm9314.
(5)
2a
2zinA01
A:188-239
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Pfam Domains
(1, 1)
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all PFAM domains
1a: PFAM_tRNA_synt_2b_2zinA01 (A:242-379)
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Clan
:
tRNA_synt_II
(64)
Family
:
tRNA-synt_2b
(25)
Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88) (Methanosarc
(7)
1a
tRNA-synt_2b-2zinA01
A:242-379
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Asym.Unit (55 KB)
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