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1B8A
Asym. Unit
Info
Asym.Unit (176 KB)
Biol.Unit 1 (170 KB)
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(1)
Title
:
ASPARTYL-TRNA SYNTHETASE
Authors
:
E. Schmitt, L. Moulinier, J. -C. Thierry, D. Moras
Date
:
27 Jan 99 (Deposition) - 02 Feb 99 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Synthetase, Trna Ligase, , Ligase
(Keyword Search:
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Reference
:
E. Schmitt, L. Moulinier, S. Fujiwara, T. Imanaka, J. C. Thierry, D. Moras
Crystal Structure Of Aspartyl-Trna Synthetase From Pyrococcus Kodakaraensis Kod: Archaeon Specificity And Catalytic Mechanism Of Adenylate Formation.
Embo J. V. 17 5227 1998
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Hetero Components
(2, 8)
Info
All Hetero Components
1a: ADENOSINE-5'-TRIPHOSPHATE (ATPa)
1b: ADENOSINE-5'-TRIPHOSPHATE (ATPb)
2a: MANGANESE (II) ION (MNa)
2b: MANGANESE (II) ION (MNb)
2c: MANGANESE (II) ION (MNc)
2d: MANGANESE (II) ION (MNd)
2e: MANGANESE (II) ION (MNe)
2f: MANGANESE (II) ION (MNf)
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Label:
No.
Name
Count
Type
Full Name
1
ATP
2
Ligand/Ion
ADENOSINE-5'-TRIPHOSPHATE
2
MN
6
Ligand/Ion
MANGANESE (II) ION
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Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ATP A:500 , HOH A:2198 , HOH A:2199 , HOH A:2200 , HOH A:2201
BINDING SITE FOR RESIDUE MN A 600
2
AC2
SOFTWARE
GLU A:361 , SER A:364 , ATP A:500 , MN A:602 , HOH A:2250 , HOH A:2251
BINDING SITE FOR RESIDUE MN A 601
3
AC3
SOFTWARE
GLU A:361 , ATP A:500 , MN A:601 , HOH A:2248 , HOH A:2249 , HOH A:2250
BINDING SITE FOR RESIDUE MN A 602
4
AC4
SOFTWARE
ATP B:1500 , HOH B:2194 , HOH B:2195 , HOH B:2196 , HOH B:2197
BINDING SITE FOR RESIDUE MN B 1600
5
AC5
SOFTWARE
GLU B:1361 , ATP B:1500 , MN B:1602 , HOH B:2252 , HOH B:2254 , HOH B:2293
BINDING SITE FOR RESIDUE MN B 1601
6
AC6
SOFTWARE
GLU B:1361 , SER B:1364 , ATP B:1500 , MN B:1601 , HOH B:2253 , HOH B:2254
BINDING SITE FOR RESIDUE MN B 1602
7
AC7
SOFTWARE
ARG A:214 , GLU A:216 , ARG A:222 , HIS A:223 , LEU A:224 , GLU A:361 , ILE A:362 , SER A:363 , SER A:364 , GLY A:407 , GLY A:409 , ARG A:412 , MN A:600 , MN A:601 , MN A:602 , HOH A:2148 , HOH A:2191 , HOH A:2199 , HOH A:2200 , HOH A:3114
BINDING SITE FOR RESIDUE ATP A 500
8
AC8
SOFTWARE
ARG B:1214 , GLU B:1216 , HIS B:1223 , LEU B:1224 , ALA B:1227 , GLU B:1361 , ILE B:1362 , SER B:1363 , SER B:1364 , GLY B:1407 , GLY B:1409 , ARG B:1412 , MN B:1600 , MN B:1601 , MN B:1602 , HOH B:2123 , HOH B:2196 , HOH B:2197 , HOH B:2987
BINDING SITE FOR RESIDUE ATP B 1500
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
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Exons
(0, 0)
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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
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1b8aa1 (A:1-103)
1b: SCOP_d1b8ab1 (B:1001-1103)
2a: SCOP_d1b8aa2 (A:104-438)
2b: SCOP_d1b8ab2 (B:1104-1438)
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Protein Domains
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(
)
Organisms
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(
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Class
:
All beta proteins
(24004)
Fold
:
OB-fold
(1179)
Superfamily
:
Nucleic acid-binding proteins
(590)
Family
:
Anticodon-binding domain
(21)
Protein domain
:
Aspartyl-tRNA synthetase (AspRS)
(11)
Pyrococcus kodakaraensis [TaxId: 311400]
(1)
1a
d1b8aa1
A:1-103
1b
d1b8ab1
B:1001-1103
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
:
Aspartyl-tRNA synthetase (AspRS)
(11)
Pyrococcus kodakaraensis [TaxId: 311400]
(1)
2a
d1b8aa2
A:104-438
2b
d1b8ab2
B:1104-1438
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1b8aA02 (A:106-438)
1b: CATH_1b8aB02 (B:1106-1438)
2a: CATH_1b8aA01 (A:1-105)
2b: CATH_1b8aB01 (B:1001-1105)
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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)
Thermococcus kodakarensis kod1. Organism_taxid: 69014. Strain: kod1.
(1)
1a
1b8aA02
A:106-438
1b
1b8aB02
B:1106-1438
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
OB fold (Dihydrolipoamide Acetyltransferase, E2P)
(1040)
Homologous Superfamily
:
Nucleic acid-binding proteins
(483)
Thermococcus kodakarensis kod1. Organism_taxid: 69014. Strain: kod1.
(1)
2a
1b8aA01
A:1-105
2b
1b8aB01
B:1001-1105
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Pfam Domains
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Asymmetric Unit 1
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