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3TY9
Asym. Unit
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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(1)
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
[
close entry info
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Hetero Components
(5, 25)
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:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AMP
4
Ligand/Ion
ADENOSINE MONOPHOSPHATE
2
GOL
1
Ligand/Ion
GLYCEROL
3
MG
4
Ligand/Ion
MAGNESIUM ION
4
MPD
10
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
5
MRD
6
Ligand/Ion
(4R)-2-METHYLPENTANE-2,4-DIOL
[
close Hetero Component info
]
Sites
(24, 24)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:529 , GLN A:530 , LYS A:531 , HIS A:532 , ARG A:536 , GLU A:607 , ARG A:687 , PHE A:704 , GLU A:769 , LYS A:774 , LYS A:792 , ARG A:794
BINDING SITE FOR RESIDUE AMP A 900
02
AC2
SOFTWARE
GLY A:767 , ILE A:801
BINDING SITE FOR RESIDUE MPD A 905
03
AC3
SOFTWARE
LEU B:489 , GLY B:567
BINDING SITE FOR RESIDUE MPD A 906
04
AC4
SOFTWARE
ARG A:551 , PHE A:842 , ASN A:845 , GLU A:846
BINDING SITE FOR RESIDUE MPD A 907
05
AC5
SOFTWARE
SER A:502 , LYS A:504 , MET A:507 , MET A:809 , GLU A:811 , GLU A:814
BINDING SITE FOR RESIDUE MRD A 908
06
AC6
SOFTWARE
ARG A:583 , ASP A:733 , ASP A:734 , SER A:735 , ARG D:819
BINDING SITE FOR RESIDUE MRD A 909
07
AC7
SOFTWARE
GLU A:684 , ARG A:687 , ILE A:802
BINDING SITE FOR RESIDUE GOL A 910
08
AC8
SOFTWARE
THR A:731 , ASP A:734 , ILE A:737
BINDING SITE FOR RESIDUE MG A 1000
09
AC9
SOFTWARE
GLU B:529 , GLN B:530 , LYS B:531 , HIS B:532 , ARG B:536 , GLU B:607 , ARG B:687 , PHE B:704 , GLU B:769 , LYS B:774 , LYS B:792 , ARG B:794
BINDING SITE FOR RESIDUE AMP B 900
10
BC1
SOFTWARE
ASP B:733
BINDING SITE FOR RESIDUE MPD B 905
11
BC2
SOFTWARE
SER B:502 , LYS B:503 , LYS B:504 , GLU B:505 , GLY B:506 , MET B:507 , GLU B:814
BINDING SITE FOR RESIDUE MRD B 907
12
BC3
SOFTWARE
TYR B:623 , GLY B:767 , GLY B:768
BINDING SITE FOR RESIDUE MRD B 908
13
BC4
SOFTWARE
THR B:731 , ASP B:734 , ILE B:737
BINDING SITE FOR RESIDUE MG B 1000
14
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
15
BC6
SOFTWARE
ARG A:631 , LEU A:634 , ARG C:631 , LEU C:634
BINDING SITE FOR RESIDUE MPD C 905
16
BC7
SOFTWARE
TYR C:623 , GLY C:767 , TYR C:798
BINDING SITE FOR RESIDUE MPD C 906
17
BC8
SOFTWARE
GLU C:684 , ARG C:687 , LYS C:688 , TYR C:798 , ILE C:802
BINDING SITE FOR RESIDUE MPD C 907
18
BC9
SOFTWARE
THR C:731 , ASP C:734 , ILE C:737
BINDING SITE FOR RESIDUE MG C 1000
19
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
20
CC2
SOFTWARE
LEU C:489 , LEU C:859 , LEU D:489 , THR D:566 , GLY D:567
BINDING SITE FOR RESIDUE MPD D 905
21
CC3
SOFTWARE
GLU D:684 , ARG D:687 , TYR D:798 , ILE D:802 , PRO D:868
BINDING SITE FOR RESIDUE MPD D 906
22
CC4
SOFTWARE
GLY D:767 , ILE D:801
BINDING SITE FOR RESIDUE MPD D 907
23
CC5
SOFTWARE
LYS B:781 , LYS D:614 , ALA D:615 , TRP D:691
BINDING SITE FOR RESIDUE MRD D 908
24
CC6
SOFTWARE
THR D:731 , ASP D:734 , ILE D:737
BINDING SITE FOR RESIDUE MG D 1000
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
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End label:
Sorry, no Info available
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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
(0, 0)
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Sorry, no Info available
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CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
[
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Asymmetric Unit 1
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select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
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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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