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2Q7E
Asym. Unit
Info
Asym.Unit (57 KB)
Biol.Unit 1 (99 KB)
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(1)
Title
:
THE STRUCTURE OF PYRROLYSYL-TRNA SYNTHETASE BOUND TO AN ATP ANALOGUE
Authors
:
J. M. Kavran, T. A. Steitz
Date
:
06 Jun 07 (Deposition) - 24 Jul 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A
Biol. Unit 1: A (2x)
Keywords
:
Aminoacyl-Trna Synthetase, Pyrrolysine, Ligase
(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, 14)
Info
All Hetero Components
1a: PHOSPHOAMINOPHOSPHONIC ACID-ADENYL... (ANPa)
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)
2k: 1,2-ETHANEDIOL (EDOk)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ANP
1
Ligand/Ion
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2
EDO
11
Ligand/Ion
1,2-ETHANEDIOL
3
MG
2
Ligand/Ion
MAGNESIUM ION
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Sites
(14, 14)
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)
View:
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ANP A:900 , HOH A:1002 , HOH A:1004 , HOH A:1006 , HOH A:1014
BINDING SITE FOR RESIDUE MG A 501
02
AC2
SOFTWARE
GLU A:396 , SER A:399 , ANP A:900 , HOH A:1117
BINDING SITE FOR RESIDUE MG A 502
03
AC3
SOFTWARE
ARG A:330 , GLU A:332 , HIS A:338 , LEU A:339 , PHE A:342 , MET A:344 , GLU A:396 , LEU A:397 , SER A:398 , SER A:399 , GLY A:421 , GLY A:423 , ARG A:426 , MG A:501 , MG A:502 , EDO A:906 , HOH A:912 , HOH A:1002 , HOH A:1004 , HOH A:1006 , HOH A:1014 , HOH A:1088 , HOH A:1106 , HOH A:1115 , HOH A:1118
BINDING SITE FOR RESIDUE ANP A 900
04
AC4
SOFTWARE
ASN A:241 , ARG A:439 , ALA A:440 , ASN A:448 , GLY A:449 , HOH A:963
BINDING SITE FOR RESIDUE EDO A 901
05
AC5
SOFTWARE
TYR A:242 , LYS A:245 , LEU A:246 , GLU A:249 , LYS A:431 , HIS A:432 , HOH A:1090
BINDING SITE FOR RESIDUE EDO A 902
06
AC6
SOFTWARE
ASP A:256 , ARG A:257 , HIS A:369 , HOH A:937
BINDING SITE FOR RESIDUE EDO A 903
07
AC7
SOFTWARE
ASP A:373 , LYS A:375 , MET A:391 , HIS A:392 , GLY A:393 , EDO A:909
BINDING SITE FOR RESIDUE EDO A 904
08
AC8
SOFTWARE
ASP A:313 , MET A:350 , GLY A:412 , ILE A:413 , ASP A:414 , LYS A:415 , HOH A:994
BINDING SITE FOR RESIDUE EDO A 905
09
AC9
SOFTWARE
HIS A:338 , ASP A:394 , GLU A:396 , ARG A:426 , ANP A:900 , HOH A:1088
BINDING SITE FOR RESIDUE EDO A 906
10
BC1
SOFTWARE
ALA A:302 , TYR A:306 , TYR A:384 , TRP A:417 , HOH A:1023
BINDING SITE FOR RESIDUE EDO A 907
11
BC2
SOFTWARE
ARG A:257 , ASP A:365 , HOH A:938 , HOH A:1105
BINDING SITE FOR RESIDUE EDO A 908
12
BC3
SOFTWARE
ASP A:373 , HIS A:392 , GLY A:393 , EDO A:904
BINDING SITE FOR RESIDUE EDO A 909
13
BC4
SOFTWARE
TYR A:272 , ASN A:307 , ARG A:310 , LYS A:311 , GLU A:357 , GLU A:444 , HOH A:987
BINDING SITE FOR RESIDUE EDO A 910
14
BC5
SOFTWARE
GLU A:237 , HOH A:1098
BINDING SITE FOR RESIDUE EDO A 911
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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
(0, 0)
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(0, 0)
Info
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CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_2q7eA02 (A:240-454)
2a: CATH_2q7eA01 (A:188-239)
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Classes
(
)
(
)
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(
)
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(
)
(
)
Homologous Superfamilies
(
)
(
)
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
2q7eA02
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
2q7eA01
A:188-239
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Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_tRNA_synt_2b_2q7eA01 (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-2q7eA01
A:242-382
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Chain A
Asymmetric Unit 1
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