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1GGM
Asym. Unit
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Asym.Unit (184 KB)
Biol.Unit 1 (178 KB)
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(1)
Title
:
GLYCYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH GLYCYL-ADENYLATE
Authors
:
J. G. Arnez, D. Moras
Date
:
27 Jan 99 (Deposition) - 28 Jan 99 (Release) - 31 May 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.40
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Aminoacyl-Trna Synthase, Ligase(Synthetase), Ligase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. G. Arnez, A. C. Dock-Bregeon, D. Moras
Glycyl-Trna Synthetase Uses A Negatively Charged Pit For Specific Recognition And Activation Of Glycine.
J. Mol. Biol. V. 286 1449 1999
(for further references see the
PDB file header
)
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Hetero Components
(1, 2)
Info
All Hetero Components
1a: GLYCYL-ADENOSINE-5'-PHOSPHATE (GAPa)
1b: GLYCYL-ADENOSINE-5'-PHOSPHATE (GAPb)
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Label:
No.
Name
Count
Type
Full Name
1
GAP
2
Ligand/Ion
GLYCYL-ADENOSINE-5'-PHOSPHATE
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: S1A (AUTHOR)
4: S1B (AUTHOR)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLU A:188 , ALA A:190 , ARG A:220 , PHE A:230 , VAL A:232 , PHE A:235 , GLN A:237 , GLU A:239 , GLU A:304 , LEU A:305 , GLU A:306 , GLU A:359 , SER A:361 , GLY A:363 , ARG A:366 , HOH A:550
BINDING SITE FOR RESIDUE GAP A 1550
2
AC2
SOFTWARE
GLU B:188 , ALA B:190 , ARG B:220 , PHE B:230 , VAL B:232 , PHE B:235 , GLN B:237 , GLU B:239 , TYR B:287 , GLU B:304 , LEU B:305 , GLU B:306 , ARG B:311 , GLU B:359 , SER B:361 , GLY B:363 , ARG B:366
BINDING SITE FOR RESIDUE GAP B 2550
3
S1A
AUTHOR
GLU A:188 , ARG A:220 , GLU A:222 , ARG A:231 , VAL A:232 , PHE A:235 , GLN A:237 , GLU A:239 , GLU A:241 , ASP A:293 , GLU A:304 , ARG A:311 , ASP A:315 , GLU A:359 , SER A:361 , ARG A:366 , GAP A:1550
GLYCINE AND ATP BINDING SITE, PRODUCT OF THE FIRST REACTION (INTERMEDIATE IN THE OVERALL REACTION):GLYCYL- ADENYLATE (OBSERVED IN THE SITE).
4
S1B
AUTHOR
GLU B:188 , ARG B:220 , GLU B:222 , ARG B:231 , VAL B:232 , PHE B:235 , GLN B:237 , GLU B:239 , GLU B:241 , ASP B:293 , GLU B:304 , ARG B:311 , ASP B:315 , GLU B:359 , SER B:361 , ARG B:366 , GAP B:2550
GLYCINE AND ATP BINDING SITE, PRODUCT OF THE FIRST REACTION (INTERMEDIATE IN THE OVERALL REACTION):GLYCYL- ADENYLATE (OBSERVED IN THE SITE).
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are not available)
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Exons
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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
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1ggma2 (A:1-394)
1b: SCOP_d1ggmb2 (B:1-394)
2a: SCOP_d1ggma1 (A:395-505)
2b: SCOP_d1ggmb1 (B:395-505)
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Protein Domains
(
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(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Class II aaRS and biotin synthetases
(165)
Superfamily
:
Class II aaRS and biotin synthetases
(165)
Family
:
Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain
(103)
Protein domain
:
Glycyl-tRNA synthetase (GlyRS)
(3)
Thermus thermophilus [TaxId: 274]
(3)
1a
d1ggma2
A:1-394
1b
d1ggmb2
B:1-394
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Anticodon-binding domain-like
(97)
Superfamily
:
Class II aaRS ABD-related
(40)
Family
:
Anticodon-binding domain of Class II aaRS
(33)
Protein domain
:
Glycyl-tRNA synthetase (GlyRS), C-terminal domain
(3)
Thermus thermophilus [TaxId: 274]
(3)
2a
d1ggma1
A:395-505
2b
d1ggmb1
B:395-505
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1ggmA01 (A:1-374)
1b: CATH_1ggmB01 (B:1-374)
2a: CATH_1ggmA02 (A:393-505)
2b: CATH_1ggmB02 (B:393-505)
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Organisms
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(
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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)
Thermus thermophilus hb8. Organism_taxid: 300852. Strain: hb8.
(4)
1a
1ggmA01
A:1-374
1b
1ggmB01
B:1-374
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.800, no name defined]
(40)
Thermus thermophilus hb8. Organism_taxid: 300852. Strain: hb8.
(2)
2a
1ggmA02
A:393-505
2b
1ggmB02
B:393-505
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Pfam Domains
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