PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
5SZD
Biol. Unit 2
Info
Asym.Unit (340 KB)
Biol.Unit 1 (166 KB)
Biol.Unit 2 (171 KB)
Biol.Unit 3 (333 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF AQUIFEX AEOLICUS HFQ AT 1.5A
Authors
:
K. Stanek, J. Patterson, P. S. Randolph, C. Mura
Date
:
13 Aug 16 (Deposition) - 19 Apr 17 (Release) - 19 Apr 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.49
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,C,D,E,F (1x)
Biol. Unit 2: G,H,I,J,K,L (1x)
Biol. Unit 3: A,B,C,D,E,F,G,H,I,J,K,L (1x)
Keywords
:
Hfq, Aquifex, Rna-Binding, Rna Binding Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. A. Stanek, J. Patterson-West, P. S. Randolph, C. Mura
Crystal Structure And Rna-Binding Properties Of An Hfq Homolog From The Deep-Branching Aquificae: Conservation Of The Lateral Rna-Binding Mode.
Acta Crystallogr D Struct V. 73 294 2017 Biol
[
close entry info
]
Hetero Components
(4, 19)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
1d: CHLORIDE ION (CLd)
1e: CHLORIDE ION (CLe)
1f: CHLORIDE ION (CLf)
1g: CHLORIDE ION (CLg)
2a: GUANIDINE (GAIa)
2b: GUANIDINE (GAIb)
2c: GUANIDINE (GAIc)
2d: GUANIDINE (GAId)
2e: GUANIDINE (GAIe)
2f: GUANIDINE (GAIf)
2g: GUANIDINE (GAIg)
2h: GUANIDINE (GAIh)
3a: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDa)
3b: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDb)
3c: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDc)
3d: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDd)
3e: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDe)
3f: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDf)
3g: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDg)
3h: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDh)
3i: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDi)
3j: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDj)
3k: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDk)
3l: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDl)
4a: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDa)
4b: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDb)
4c: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDc)
4d: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDd)
4e: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDe)
4f: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDf)
4g: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDg)
4h: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDh)
4i: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDi)
4j: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDj)
4k: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDk)
4l: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDl)
4m: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDm)
5a: DI(HYDROXYETHYL)ETHER (PEGa)
5b: DI(HYDROXYETHYL)ETHER (PEGb)
5c: DI(HYDROXYETHYL)ETHER (PEGc)
5d: DI(HYDROXYETHYL)ETHER (PEGd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
-1
Ligand/Ion
CHLORIDE ION
2
GAI
2
Ligand/Ion
GUANIDINE
3
MPD
7
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
4
MRD
6
Ligand/Ion
(4R)-2-METHYLPENTANE-2,4-DIOL
5
PEG
4
Ligand/Ion
DI(HYDROXYETHYL)ETHER
[
close Hetero Component info
]
Sites
(30, 30)
Info
All Sites
01: AC4 (SOFTWARE)
02: AC8 (SOFTWARE)
03: AD2 (SOFTWARE)
04: AD7 (SOFTWARE)
05: AE1 (SOFTWARE)
06: AE2 (SOFTWARE)
07: AE3 (SOFTWARE)
08: AE4 (SOFTWARE)
09: AE5 (SOFTWARE)
10: AE6 (SOFTWARE)
11: AE7 (SOFTWARE)
12: AE8 (SOFTWARE)
13: AE9 (SOFTWARE)
14: AF1 (SOFTWARE)
15: AF2 (SOFTWARE)
16: AF3 (SOFTWARE)
17: AF4 (SOFTWARE)
18: AF5 (SOFTWARE)
19: AF6 (SOFTWARE)
20: AF7 (SOFTWARE)
21: AF8 (SOFTWARE)
22: AF9 (SOFTWARE)
23: AG1 (SOFTWARE)
24: AG2 (SOFTWARE)
25: AG3 (SOFTWARE)
26: AG4 (SOFTWARE)
27: AG5 (SOFTWARE)
28: AG6 (SOFTWARE)
29: AG7 (SOFTWARE)
30: AG8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC4
SOFTWARE
ASN A:29 , GLY A:30 , LEU I:42 , TYR J:6
binding site for residue GAI A 104
02
AC8
SOFTWARE
ASN B:29 , GLY B:30 , TYR K:6
binding site for residue GAI B 103
03
AD2
SOFTWARE
ASN C:29 , GLY C:30 , LEU K:42 , TYR L:6
binding site for residue GAI C 103
04
AD7
SOFTWARE
ASN E:29 , GLY E:30 , HOH E:222 , TYR H:6
binding site for residue GAI E 103
05
AE1
SOFTWARE
ASN F:29 , GLY F:30 , HOH F:206 , LEU H:42 , TYR I:6
binding site for residue GAI F 103
06
AE2
SOFTWARE
PHE G:43 , TYR G:57 , HIS G:59 , HOH G:216 , GLN H:9 , LEU H:42
binding site for residue MRD G 101
07
AE3
SOFTWARE
GLN G:9 , PHE G:40 , ASP G:41 , LYS G:58 , HOH G:214
binding site for residue MPD G 102
08
AE4
SOFTWARE
HOH D:207 , HOH D:217 , MET G:4 , TYR G:6 , HOH G:215
binding site for residue CL G 103
09
AE5
SOFTWARE
ASN D:29 , GLY D:30 , HOH D:216 , TYR G:6
binding site for residue GAI G 104
10
AE6
SOFTWARE
TYR G:26 , LEU G:27 , THR G:62 , THR G:63 , HOH G:208 , ASN L:29 , VAL L:31
binding site for residue PEG G 105
11
AE7
SOFTWARE
PHE H:43 , TYR H:57 , HIS H:59 , HOH H:217 , GLN I:9 , LEU I:42
binding site for residue MRD H 101
12
AE8
SOFTWARE
GLN H:9 , GLU H:10 , PHE H:40 , ASP H:41 , LYS H:58 , HOH H:221 , SER I:2
binding site for residue MPD H 102
13
AE9
SOFTWARE
GLN G:52 , TYR H:26 , THR H:63
binding site for residue MPD H 103
14
AF1
SOFTWARE
HOH E:210 , HOH E:214 , MET H:4 , TYR H:6 , HOH H:202
binding site for residue CL H 104
15
AF2
SOFTWARE
TYR H:26 , GLY H:30
binding site for residue GAI H 105
16
AF3
SOFTWARE
PHE I:43 , TYR I:57 , HIS I:59 , HOH I:216 , GLN J:9 , LEU J:42
binding site for residue MRD I 101
17
AF4
SOFTWARE
GLN I:9 , PHE I:40 , ASP I:41 , LEU I:42 , LYS I:58 , HOH I:214 , SER J:2
binding site for residue MPD I 102
18
AF5
SOFTWARE
HOH F:208 , HOH F:214 , MET I:4 , TYR I:6 , HOH I:209
binding site for residue CL I 103
19
AF6
SOFTWARE
PHE J:43 , TYR J:57 , HIS J:59 , HOH J:216 , GLN K:9 , LEU K:42
binding site for residue MRD J 101
20
AF7
SOFTWARE
GLN J:9 , PHE J:40 , ASP J:41 , LYS J:58 , HOH J:214 , SER K:2
binding site for residue MPD J 102
21
AF8
SOFTWARE
HOH A:207 , HOH A:214 , MET J:4 , TYR J:6 , LYS J:7 , HOH J:206
binding site for residue CL J 103
22
AF9
SOFTWARE
ASN I:29 , TYR J:26 , LEU J:27 , THR J:62 , THR J:63 , HOH J:201
binding site for residue PEG J 104
23
AG1
SOFTWARE
PHE K:43 , TYR K:57 , HIS K:59 , HOH K:211 , GLN L:9 , LEU L:42
binding site for residue MRD K 101
24
AG2
SOFTWARE
GLN K:9 , PHE K:40 , ASP K:41 , LYS K:58 , HOH K:209 , SER L:2
binding site for residue MPD K 102
25
AG3
SOFTWARE
HOH B:213 , HOH B:216 , MET K:4 , TYR K:6 , LYS K:7 , HOH K:207
binding site for residue CL K 103
26
AG4
SOFTWARE
LEU J:27 , ASN J:29 , LEU J:33 , LEU K:27 , THR K:62 , THR K:63 , HOH K:201 , HOH K:222
binding site for residue PEG K 104
27
AG5
SOFTWARE
GLN G:9 , LEU G:42 , PHE L:43 , TYR L:57 , HIS L:59 , HOH L:222
binding site for residue MRD L 101
28
AG6
SOFTWARE
SER G:2 , GLN L:9 , PHE L:40 , ASP L:41 , LEU L:42 , LYS L:58 , HOH L:218
binding site for residue MPD L 102
29
AG7
SOFTWARE
HOH C:207 , HOH C:215 , MET L:4 , TYR L:6 , LYS L:7 , HOH L:213
binding site for residue CL L 103
30
AG8
SOFTWARE
LEU K:27 , ASN K:29 , VAL K:31 , TYR L:26 , LEU L:27 , THR L:62 , THR L:63 , HOH L:206 , HOH L:208
binding site for residue PEG L 104
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
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
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain G
Chain H
Chain I
Chain J
Chain K
Chain L
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
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)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (340 KB)
Header - Asym.Unit
Biol.Unit 1 (166 KB)
Header - Biol.Unit 1
Biol.Unit 2 (171 KB)
Header - Biol.Unit 2
Biol.Unit 3 (333 KB)
Header - Biol.Unit 3
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
5SZD
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
