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2ZIM
Asym. Unit
Info
Asym.Unit (57 KB)
Biol.Unit 1 (99 KB)
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(1)
Title
:
PYRROLYSYL-TRNA SYNTHETASE BOUND TO ADENYLATED PYRROLYSINE AND PYROPHOSPHATE
Authors
:
T. A. Steitz, J. M. Kavran
Date
:
19 Feb 08 (Deposition) - 04 Mar 08 (Release) - 10 Aug 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A
Biol. Unit 1: A (2x)
Keywords
:
Trna Synthetase Bound To An Adenylated Intermediate, Aminoacyl-Trna Synthetase, Atp-Binding, Ligase, Nucleotide-Binding, Protein Biosynthesis
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. M. Kavran, S. Gundllapalli, P. O'Donoghue, M. Englert, D. Soll, T. A. Steitz
Structure Of Pyrrolysyl-Trna Synthetase, An Archaeal Enzyme For Genetic Code Innovation.
Proc. Natl. Acad. Sci. Usa V. 104 11268 2007
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Hetero Components
(3, 12)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1b: 1,2-ETHANEDIOL (EDOb)
1c: 1,2-ETHANEDIOL (EDOc)
1d: 1,2-ETHANEDIOL (EDOd)
1e: 1,2-ETHANEDIOL (EDOe)
1f: 1,2-ETHANEDIOL (EDOf)
1g: 1,2-ETHANEDIOL (EDOg)
1h: 1,2-ETHANEDIOL (EDOh)
1i: 1,2-ETHANEDIOL (EDOi)
1j: 1,2-ETHANEDIOL (EDOj)
2a: PYROPHOSPHATE 2- (POPa)
3a: (2R)-2-AMINO-6-({[(2S,3R)-3-METHYL... (YLYa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
10
Ligand/Ion
1,2-ETHANEDIOL
2
POP
1
Ligand/Ion
PYROPHOSPHATE 2-
3
YLY
1
Ligand/Ion
(2R)-2-AMINO-6-({[(2S,3R)-3-METHYLPYRROLIDIN-2-YL]CARBONYL}AMINO)HEXANOYL [(2S,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL HYDROGEN (R)-PHOSPHATE
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Sites
(12, 12)
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)
View:
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:241 , ARG A:439 , ALA A:440 , ALA A:441 , ASN A:448 , GLY A:449 , HOH A:961
BINDING SITE FOR RESIDUE EDO A 902
02
AC2
SOFTWARE
TYR A:242 , LYS A:245 , LEU A:246 , GLU A:249 , LEU A:428 , LYS A:431 , HIS A:432
BINDING SITE FOR RESIDUE EDO A 903
03
AC3
SOFTWARE
PHE A:253 , ASP A:256 , ARG A:257 , HIS A:369 , HOH A:936 , HOH A:1061
BINDING SITE FOR RESIDUE EDO A 904
04
AC4
SOFTWARE
ASP A:373 , PHE A:374 , LYS A:375 , HIS A:392 , GLY A:393 , HOH A:1093
BINDING SITE FOR RESIDUE EDO A 905
05
AC5
SOFTWARE
ASP A:313 , MET A:350 , GLY A:412 , ILE A:413 , ASP A:414 , LYS A:415 , HOH A:991
BINDING SITE FOR RESIDUE EDO A 906
06
AC6
SOFTWARE
GLU A:337 , HIS A:338 , ASP A:394 , LEU A:395 , GLU A:396 , ARG A:426
BINDING SITE FOR RESIDUE EDO A 907
07
AC7
SOFTWARE
ARG A:257 , ILE A:362 , ASP A:365 , HOH A:937 , HOH A:1080
BINDING SITE FOR RESIDUE EDO A 908
08
AC8
SOFTWARE
ASP A:373 , HIS A:392
BINDING SITE FOR RESIDUE EDO A 909
09
AC9
SOFTWARE
TYR A:272 , ASN A:307 , ARG A:310 , LYS A:311 , GLU A:357 , HOH A:984
BINDING SITE FOR RESIDUE EDO A 910
10
BC1
SOFTWARE
GLN A:233 , ALA A:236 , GLU A:237 , HOH A:1075
BINDING SITE FOR RESIDUE EDO A 911
11
BC2
SOFTWARE
MET A:300 , ALA A:302 , LEU A:305 , TYR A:306 , ARG A:330 , GLU A:332 , LEU A:339 , PHE A:342 , MET A:344 , ASN A:346 , TYR A:384 , GLU A:396 , LEU A:397 , SER A:398 , SER A:399 , TRP A:417 , GLY A:419 , GLY A:421 , GLY A:423 , ARG A:426 , HOH A:912 , HOH A:1086 , HOH A:1094
BINDING SITE FOR RESIDUE YLY A 1
12
BC3
SOFTWARE
ARG A:330 , HIS A:338 , GLU A:396 , ARG A:426 , HOH A:1094
BINDING SITE FOR RESIDUE POP A 901
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
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Exons
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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
(0, 0)
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CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_2zimA02 (A:240-454)
2a: CATH_2zimA01 (A:188-239)
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(
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(
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(
)
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)
(
)
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)
(
)
Organisms
(
)
(
)
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.
(4)
1a
2zimA02
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.
(4)
2a
2zimA01
A:188-239
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Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_tRNA_synt_2b_2zimA01 (A:242-382)
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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-2zimA01
A:242-382
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Chain A
Asymmetric Unit 1
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