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1KMM
Biol. Unit 1
Info
Asym.Unit (297 KB)
Biol.Unit 1 (148 KB)
Biol.Unit 2 (148 KB)
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(1)
Title
:
HISTIDYL-TRNA SYNTHETASE COMPLEXED WITH HISTIDYL-ADENYLATE
Authors
:
J. G. Arnez, C. S. Francklyn, D. Moras
Date
:
09 May 97 (Deposition) - 17 Dec 97 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Aminoacyl-Trna Synthase, Ligase, Synthetase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. G. Arnez, J. G. Augustine, D. Moras, C. S. Francklyn
The First Step Of Aminoacylation At The Atomic Level In Histidyl-Trna Synthetase.
Proc. Natl. Acad. Sci. Usa V. 94 7144 1997
(for further references see the
PDB file header
)
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Hetero Components
(1, 2)
Info
All Hetero Components
1a: HISTIDYL-ADENOSINE MONOPHOSPHATE (HAMa)
1b: HISTIDYL-ADENOSINE MONOPHOSPHATE (HAMb)
1c: HISTIDYL-ADENOSINE MONOPHOSPHATE (HAMc)
1d: HISTIDYL-ADENOSINE MONOPHOSPHATE (HAMd)
View:
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Label:
No.
Name
Count
Type
Full Name
1
HAM
2
Ligand/Ion
HISTIDYL-ADENOSINE MONOPHOSPHATE
[
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: S1A (UNKNOWN)
4: S1B (UNKNOWN)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLU A:83 , THR A:85 , ARG A:113 , GLU A:115 , GLY A:120 , ARG A:121 , TYR A:122 , PHE A:125 , GLN A:127 , GLU A:131 , ARG A:259 , LEU A:261 , TYR A:263 , TYR A:264 , THR A:281 , VAL A:282 , ALA A:284 , GLY A:285 , GLY A:304 , PHE A:305 , ALA A:306 , GLY A:308 , ARG A:311 , HOH A:640
BINDING SITE FOR RESIDUE HAM A 450
2
AC2
SOFTWARE
GLU B:83 , THR B:85 , ARG B:113 , GLU B:115 , GLY B:120 , ARG B:121 , TYR B:122 , PHE B:125 , GLN B:127 , GLU B:131 , ARG B:259 , LEU B:261 , TYR B:263 , TYR B:264 , THR B:281 , VAL B:282 , ALA B:284 , GLY B:304 , PHE B:305 , GLY B:308 , ARG B:311 , HOH B:617
BINDING SITE FOR RESIDUE HAM B 450
3
S1A
UNKNOWN
GLU A:83 , THR A:85 , ARG A:113 , GLU A:115 , ARG A:121 , TYR A:122 , PHE A:125 , GLN A:127 , GLU A:131 , ARG A:259 , TYR A:263 , TYR A:264 , GLU A:270 , THR A:281 , TYR A:288 , ARG A:311 , HAM A:450
HISTIDINE AND ATP BINDING SITE, PRODUCT OF THE FIRST REACTION (INTERMEDIATE IN THE OVERALL REACTION): HISTIDYL-ADENYLATE (OBSERVED IN THE SITE).
4
S1B
UNKNOWN
GLU B:83 , THR B:85 , ARG B:113 , GLU B:115 , ARG B:121 , TYR B:122 , PHE B:125 , GLN B:127 , GLU B:131 , ARG B:259 , TYR B:263 , TYR B:264 , GLU B:270 , THR B:281 , TYR B:288 , ARG B:311 , HAM B:450
HISTIDINE AND ATP BINDING SITE, PRODUCT OF THE FIRST REACTION (INTERMEDIATE IN THE OVERALL REACTION): HISTIDYL-ADENYLATE (OBSERVED IN THE SITE).
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1kmma2 (A:4-325)
1b: SCOP_d1kmmb2 (B:2-325)
1c: SCOP_d1kmmc2 (C:4-325)
1d: SCOP_d1kmmd2 (D:4-325)
2a: SCOP_d1kmma1 (A:326-424)
2b: SCOP_d1kmmb1 (B:326-424)
2c: SCOP_d1kmmc1 (C:326-424)
2d: SCOP_d1kmmd1 (D:326-424)
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Protein Domains
(
)
(
)
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
:
Histidyl-tRNA synthetase (HisRS)
(9)
Escherichia coli [TaxId: 562]
(4)
1a
d1kmma2
A:4-325
1b
d1kmmb2
B:2-325
1c
d1kmmc2
C:4-325
1d
d1kmmd2
D:4-325
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
:
Histidyl-tRNA synthetase (HisRS), C-terminal domain
(9)
Escherichia coli [TaxId: 562]
(4)
2a
d1kmma1
A:326-424
2b
d1kmmb1
B:326-424
2c
d1kmmc1
C:326-424
2d
d1kmmd1
D:326-424
[
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]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1kmmA01 (A:4-325)
1b: CATH_1kmmC01 (C:4-325)
1c: CATH_1kmmB01 (B:4-325)
1d: CATH_1kmmD01 (D:4-325)
2a: CATH_1kmmA02 (A:326-422)
2b: CATH_1kmmB02 (B:326-422)
2c: CATH_1kmmC02 (C:326-422)
2d: CATH_1kmmD02 (D:326-422)
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Organisms
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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)
Escherichia coli. Organism_taxid: 562. Strain: jm109.
(3)
1a
1kmmA01
A:4-325
1b
1kmmC01
C:4-325
1c
1kmmB01
B:4-325
1d
1kmmD01
D:4-325
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.800, no name defined]
(40)
Escherichia coli. Organism_taxid: 562. Strain: jm109.
(3)
2a
1kmmA02
A:326-422
2b
1kmmB02
B:326-422
2c
1kmmC02
C:326-422
2d
1kmmD02
D:326-422
[
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Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_HGTP_anticodon_1kmmD01 (D:329-422)
1b: PFAM_HGTP_anticodon_1kmmD02 (D:329-422)
1c: PFAM_HGTP_anticodon_1kmmD03 (D:329-422)
1d: PFAM_HGTP_anticodon_1kmmD04 (D:329-422)
2a: PFAM_tRNA_synt_2b_1kmmD05 (D:21-169)
2b: PFAM_tRNA_synt_2b_1kmmD06 (D:21-169)
2c: PFAM_tRNA_synt_2b_1kmmD07 (D:21-169)
2d: PFAM_tRNA_synt_2b_1kmmD08 (D:21-169)
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)
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)
Clan
:
IIaaRS-ABD
(13)
Family
:
HGTP_anticodon
(13)
Escherichia coli (strain K12)
(4)
1a
HGTP_anticodon-1kmmD01
D:329-422
1b
HGTP_anticodon-1kmmD02
D:329-422
1c
HGTP_anticodon-1kmmD03
D:329-422
1d
HGTP_anticodon-1kmmD04
D:329-422
Clan
:
tRNA_synt_II
(64)
Family
:
tRNA-synt_2b
(25)
Escherichia coli (strain K12)
(4)
2a
tRNA-synt_2b-1kmmD05
D:21-169
2b
tRNA-synt_2b-1kmmD06
D:21-169
2c
tRNA-synt_2b-1kmmD07
D:21-169
2d
tRNA-synt_2b-1kmmD08
D:21-169
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Asym.Unit (297 KB)
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