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3TY9
Biol. Unit 4
Info
Asym.Unit (258 KB)
Biol.Unit 1 (128 KB)
Biol.Unit 2 (127 KB)
Biol.Unit 3 (127 KB)
Biol.Unit 4 (128 KB)
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Title
:
CRYSTAL STRUCTURE OF C. THERMOCELLUM PNKP LIGASE DOMAIN AMP-ADENYLATE
Authors
:
P. Smith, L. Wang, S. Shuman
Date
:
24 Sep 11 (Deposition) - 25 Jan 12 (Release) - 29 Feb 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.12
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,C (1x)
Biol. Unit 2: A,B (1x)
Biol. Unit 3: B,D (1x)
Biol. Unit 4: C,D (1x)
Keywords
:
Dna Ligase/Mrna Capping Enzyme, Rna Ligase, Adenylyltransferase, Hen1, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. Smith, L. K. Wang, P. A. Nair, S. Shuman
The Adenylyltransferase Domain Of Bacterial Pnkp Defines A Unique Rna Ligase Family.
Proc. Natl. Acad. Sci. Usa V. 109 2296 2012
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Hetero Components
(3, 9)
Info
All Hetero Components
1a: ADENOSINE MONOPHOSPHATE (AMPa)
1b: ADENOSINE MONOPHOSPHATE (AMPb)
1c: ADENOSINE MONOPHOSPHATE (AMPc)
1d: ADENOSINE MONOPHOSPHATE (AMPd)
2a: GLYCEROL (GOLa)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
4a: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDa)
4b: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDb)
4c: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDc)
4d: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDd)
4e: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDe)
4f: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDf)
4g: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDg)
4h: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDh)
4i: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDi)
4j: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDj)
5a: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDa)
5b: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDb)
5c: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDc)
5d: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDd)
5e: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDe)
5f: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDf)
View:
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Label:
No.
Name
Count
Type
Full Name
1
AMP
2
Ligand/Ion
ADENOSINE MONOPHOSPHATE
2
GOL
-1
Ligand/Ion
GLYCEROL
3
MG
-1
Ligand/Ion
MAGNESIUM ION
4
MPD
6
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
5
MRD
1
Ligand/Ion
(4R)-2-METHYLPENTANE-2,4-DIOL
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Sites
(12, 12)
Info
All Sites
01: AC6 (SOFTWARE)
02: BC5 (SOFTWARE)
03: BC6 (SOFTWARE)
04: BC7 (SOFTWARE)
05: BC8 (SOFTWARE)
06: BC9 (SOFTWARE)
07: CC1 (SOFTWARE)
08: CC2 (SOFTWARE)
09: CC3 (SOFTWARE)
10: CC4 (SOFTWARE)
11: CC5 (SOFTWARE)
12: CC6 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC6
SOFTWARE
ARG A:583 , ASP A:733 , ASP A:734 , SER A:735 , ARG D:819
BINDING SITE FOR RESIDUE MRD A 909
02
BC5
SOFTWARE
GLU C:529 , GLN C:530 , LYS C:531 , HIS C:532 , ARG C:536 , GLU C:607 , ARG C:687 , PHE C:704 , GLU C:769 , LYS C:774 , LYS C:792 , ARG C:794
BINDING SITE FOR RESIDUE AMP C 900
03
BC6
SOFTWARE
ARG A:631 , LEU A:634 , ARG C:631 , LEU C:634
BINDING SITE FOR RESIDUE MPD C 905
04
BC7
SOFTWARE
TYR C:623 , GLY C:767 , TYR C:798
BINDING SITE FOR RESIDUE MPD C 906
05
BC8
SOFTWARE
GLU C:684 , ARG C:687 , LYS C:688 , TYR C:798 , ILE C:802
BINDING SITE FOR RESIDUE MPD C 907
06
BC9
SOFTWARE
THR C:731 , ASP C:734 , ILE C:737
BINDING SITE FOR RESIDUE MG C 1000
07
CC1
SOFTWARE
GLU D:529 , GLN D:530 , LYS D:531 , HIS D:532 , ARG D:536 , GLU D:607 , ARG D:687 , PHE D:704 , GLU D:769 , LYS D:774 , LYS D:792 , ARG D:794
BINDING SITE FOR RESIDUE AMP D 900
08
CC2
SOFTWARE
LEU C:489 , LEU C:859 , LEU D:489 , THR D:566 , GLY D:567
BINDING SITE FOR RESIDUE MPD D 905
09
CC3
SOFTWARE
GLU D:684 , ARG D:687 , TYR D:798 , ILE D:802 , PRO D:868
BINDING SITE FOR RESIDUE MPD D 906
10
CC4
SOFTWARE
GLY D:767 , ILE D:801
BINDING SITE FOR RESIDUE MPD D 907
11
CC5
SOFTWARE
LYS B:781 , LYS D:614 , ALA D:615 , TRP D:691
BINDING SITE FOR RESIDUE MRD D 908
12
CC6
SOFTWARE
THR D:731 , ASP D:734 , ILE D:737
BINDING SITE FOR RESIDUE MG D 1000
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
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Exons
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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SCOP Domains
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CATH Domains
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Pfam Domains
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Asymmetric Unit 1
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Show PDB file:
Asym.Unit (258 KB)
Header - Asym.Unit
Biol.Unit 1 (128 KB)
Header - Biol.Unit 1
Biol.Unit 2 (127 KB)
Header - Biol.Unit 2
Biol.Unit 3 (127 KB)
Header - Biol.Unit 3
Biol.Unit 4 (128 KB)
Header - Biol.Unit 4
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