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1KMM
Asym. Unit
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, 4)
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:
Select:
Label:
No.
Name
Count
Type
Full Name
1
HAM
4
Ligand/Ion
HISTIDYL-ADENOSINE MONOPHOSPHATE
[
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]
Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: S1A (UNKNOWN)
6: S1B (UNKNOWN)
7: S1C (UNKNOWN)
8: S1D (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
AC3
SOFTWARE
GLU C:83 , THR C:85 , ARG C:113 , GLU C:115 , GLY C:120 , ARG C:121 , TYR C:122 , PHE C:125 , GLN C:127 , GLU C:131 , ARG C:259 , LEU C:261 , TYR C:263 , TYR C:264 , THR C:281 , VAL C:282 , ALA C:284 , GLY C:285 , GLY C:304 , PHE C:305 , ALA C:306 , GLY C:308 , ARG C:311 , HOH C:508 , HOH C:623 , HOH C:678
BINDING SITE FOR RESIDUE HAM C 450
4
AC4
SOFTWARE
GLU D:83 , THR D:85 , ARG D:113 , GLU D:115 , GLY D:120 , ARG D:121 , TYR D:122 , PHE D:125 , GLN D:127 , GLU D:131 , ARG D:259 , TYR D:263 , TYR D:264 , THR D:281 , VAL D:282 , GLY D:285 , GLY D:304 , PHE D:305 , GLY D:308 , ARG D:311
BINDING SITE FOR RESIDUE HAM D 450
5
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).
6
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).
7
S1C
UNKNOWN
GLU C:83 , THR C:85 , ARG C:113 , GLU C:115 , ARG C:121 , TYR C:122 , PHE C:125 , GLN C:127 , GLU C:131 , ARG C:259 , TYR C:263 , TYR C:264 , GLU C:270 , THR C:281 , TYR C:288 , ARG C:311 , HAM C:450
HISTIDINE AND ATP BINDING SITE, PRODUCT OF THE FIRST REACTION (INTERMEDIATE IN THE OVERALL REACTION): HISTIDYL-ADENYLATE (OBSERVED IN THE SITE).
8
S1D
UNKNOWN
GLU D:83 , THR D:85 , ARG D:113 , GLU D:115 , ARG D:121 , TYR D:122 , PHE D:125 , GLN D:127 , GLU D:131 , ARG D:259 , TYR D:263 , TYR D:264 , GLU D:270 , THR D:281 , TYR D:288 , ARG D:311 , HAM D: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)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
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Exons
(0, 0)
Info
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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, 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
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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
:
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
[
close SCOP info
]
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
(
)
(
)
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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)
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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