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.
PLEASE WAIT...
Getting 'Exon' information from database.
5M67
Asym. Unit
Info
Asym.Unit (653 KB)
Biol.Unit 1 (643 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 S-ADENOSYL-L-HOMOCYSTEINE HYDROLASE FROM BRADYRHIZOBIUM ELKANII IN COMPLEX WITH ADENINE AND 2'-DEOXYADENOSINE
Authors
:
T. Manszewski, M. Jaskolski
Date
:
24 Oct 16 (Deposition) - 10 May 17 (Release) - 31 May 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.54
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Sahase, Hydrolase, Sah, Sam-Dependent Methylation, Nitrogen Fixation, Symbiotic Bacteria, Nad, Conformational Transition, Molecular Gate, Adenine, 2`-Deoxyadenosine
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Manszewski, K. Szpotkowski, M. Jaskolski
Crystallographic And Saxs Studies Of S-Adenosyl-L-Homocysteine Hydrolase From Bradyrhizobium Elkanii.
Iucrj V. 4 271 2017
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(6, 18)
Info
All Hetero Components
1a: (2R,3S,5R)-5-(6-AMINO-9H-PURIN-9-Y... (3D1a)
1b: (2R,3S,5R)-5-(6-AMINO-9H-PURIN-9-Y... (3D1b)
2a: ACETATE ION (ACTa)
2b: ACETATE ION (ACTb)
3a: ADENINE (ADEa)
3b: ADENINE (ADEb)
5a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
5b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
5c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
5d: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADd)
4a: SODIUM ION (NAa)
4b: SODIUM ION (NAb)
4c: SODIUM ION (NAc)
4d: SODIUM ION (NAd)
5e: SODIUM ION (NAe)
6a: DI(HYDROXYETHYL)ETHER (PEGa)
6b: DI(HYDROXYETHYL)ETHER (PEGb)
6c: DI(HYDROXYETHYL)ETHER (PEGc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
3D1
2
Ligand/Ion
(2R,3S,5R)-5-(6-AMINO-9H-PURIN-9-YL)-TETRAHYDRO-2-(HYDROXYMETHYL)FURAN-3-OL
2
ACT
2
Ligand/Ion
ACETATE ION
3
ADE
2
Ligand/Ion
ADENINE
4
NA
5
Ligand/Ion
SODIUM ION
5
NAD
4
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
6
PEG
3
Ligand/Ion
DI(HYDROXYETHYL)ETHER
[
close Hetero Component info
]
Sites
(18, 18)
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: AD1 (SOFTWARE)
11: AD2 (SOFTWARE)
12: AD3 (SOFTWARE)
13: AD4 (SOFTWARE)
14: AD5 (SOFTWARE)
15: AD6 (SOFTWARE)
16: AD7 (SOFTWARE)
17: AD8 (SOFTWARE)
18: AD9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLN A:62 , MET A:390 , HIS A:392 , HOH A:878 , HOH A:922 , HOH C:814
binding site for residue NA A 501
02
AC2
SOFTWARE
HOH A:846 , HOH A:1038 , HOH B:783 , HOH C:807 , HOH D:791 , HOH D:994
binding site for residue NA A 502
03
AC3
SOFTWARE
THR A:198 , THR A:199 , THR A:200 , ASN A:232 , GLY A:263 , ASP A:264 , VAL A:265 , SER A:283 , GLU A:284 , VAL A:285 , ASP A:286 , CYS A:289 , THR A:317 , GLY A:318 , ASN A:319 , ILE A:322 , ILE A:340 , GLY A:341 , HIS A:342 , LEU A:383 , ASN A:385 , HIS A:392 , ADE A:504 , HOH A:696 , HOH A:747 , HOH A:749 , HOH A:766 , HOH A:782 , HOH A:829 , HOH A:862 , GLN B:454 , LYS B:467 , TYR B:471
binding site for residue NAD A 503
04
AC4
SOFTWARE
HIS A:58 , THR A:60 , GLN A:62 , THR A:63 , LEU A:386 , MET A:390 , HIS A:392 , MET A:397 , PHE A:401 , NAD A:503 , HOH A:604 , HOH A:729 , HOH A:835
binding site for residue ADE A 504
05
AC5
SOFTWARE
ARG A:237 , GLN A:275 , HOH A:603 , HOH A:620 , HOH A:812 , HOH A:970 , ARG C:245 , GLN C:275 , ALA C:276 , GLY C:277
binding site for residue PEG A 505
06
AC6
SOFTWARE
GLN B:62 , MET B:390 , HIS B:392 , HOH B:847 , HOH B:899 , HOH D:842
binding site for residue NA B 501
07
AC7
SOFTWARE
LYS A:467 , TYR A:471 , THR B:198 , THR B:199 , THR B:200 , ASN B:232 , GLY B:261 , GLY B:263 , ASP B:264 , VAL B:265 , SER B:283 , GLU B:284 , VAL B:285 , ASP B:286 , CYS B:289 , ALA B:316 , THR B:317 , GLY B:318 , ASN B:319 , ILE B:322 , ILE B:340 , GLY B:341 , HIS B:342 , LEU B:383 , ASN B:385 , HIS B:392 , ADE B:503 , HOH B:662 , HOH B:671 , HOH B:677 , HOH B:778 , HOH B:801 , HOH B:811 , HOH B:957
binding site for residue NAD B 502
08
AC8
SOFTWARE
HIS B:58 , THR B:60 , GLN B:62 , THR B:63 , MET B:390 , HIS B:392 , MET B:397 , PHE B:401 , NAD B:502 , HOH B:614 , HOH B:641 , HOH B:709
binding site for residue ADE B 503
09
AC9
SOFTWARE
PHE B:20 , LYS B:23 , HOH B:685 , HOH B:766 , ILE D:360 , LYS D:361 , HOH D:816
binding site for residue PEG B 504
10
AD1
SOFTWARE
ASP B:344 , ILE B:349 , ARG B:353 , ARG B:382 , HOH B:687
binding site for residue ACT B 505
11
AD2
SOFTWARE
HOH A:828 , GLN C:62 , MET C:390 , HIS C:392 , HOH C:791 , HOH C:878
binding site for residue NA C 501
12
AD3
SOFTWARE
THR C:198 , THR C:199 , THR C:200 , ASN C:232 , GLY C:263 , ASP C:264 , VAL C:265 , SER C:283 , GLU C:284 , VAL C:285 , ASP C:286 , CYS C:289 , THR C:317 , GLY C:318 , ASN C:319 , ILE C:322 , ILE C:340 , GLY C:341 , HIS C:342 , LEU C:383 , ASN C:385 , HIS C:392 , 3D1 C:503 , HOH C:696 , HOH C:717 , HOH C:722 , HOH C:726 , HOH C:733 , HOH C:759 , HOH C:800 , GLN D:454 , LYS D:467 , TYR D:471
binding site for residue NAD C 502
13
AD4
SOFTWARE
LEU C:57 , HIS C:58 , THR C:60 , GLN C:62 , THR C:63 , ASP C:135 , GLU C:197 , THR C:198 , LYS C:227 , ASP C:231 , HIS C:342 , LEU C:383 , MET C:390 , HIS C:392 , MET C:397 , PHE C:401 , NAD C:502 , HOH C:609
binding site for residue 3D1 C 503
14
AD5
SOFTWARE
ASP C:344 , ILE C:349 , ARG C:353 , ARG C:382 , HOH C:601 , HOH C:645
binding site for residue ACT C 504
15
AD6
SOFTWARE
HOH B:815 , GLN D:62 , MET D:390 , HIS D:392 , HOH D:766 , HOH D:898
binding site for residue NA D 501
16
AD7
SOFTWARE
LEU C:450 , GLN C:454 , LYS C:467 , TYR C:471 , THR D:198 , THR D:199 , THR D:200 , ASN D:232 , GLY D:263 , ASP D:264 , VAL D:265 , SER D:283 , GLU D:284 , VAL D:285 , ASP D:286 , CYS D:289 , THR D:317 , GLY D:318 , ASN D:319 , ILE D:322 , ILE D:340 , GLY D:341 , HIS D:342 , LEU D:383 , ASN D:385 , HIS D:392 , 3D1 D:503 , HOH D:715 , HOH D:724 , HOH D:753 , HOH D:782 , HOH D:783 , HOH D:803 , HOH D:949
binding site for residue NAD D 502
17
AD8
SOFTWARE
HIS D:58 , THR D:60 , GLN D:62 , THR D:63 , ASP D:135 , GLU D:197 , THR D:198 , LYS D:227 , ASP D:231 , HIS D:342 , MET D:390 , HIS D:392 , MET D:397 , PHE D:401 , NAD D:502 , HOH D:609 , HOH D:621
binding site for residue 3D1 D 503
18
AD9
SOFTWARE
ARG B:245 , GLN B:275 , ALA B:276 , GLY B:277 , ARG D:237 , GLN D:275 , HOH D:605 , HOH D:615 , HOH D:674 , HOH D:990
binding site for residue PEG D 504
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(0, 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.
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 A
Chain B
Chain C
Chain D
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 (653 KB)
Header - Asym.Unit
Biol.Unit 1 (643 KB)
Header - Biol.Unit 1
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
5M67
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
