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.
5M1I
Asym. Unit
Info
Asym.Unit (106 KB)
Biol.Unit 1 (100 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF GH36 ALPHA-GALACTOSIDASE FROM THERMOTOGA MARITIMA IN A COVALENT COMPLEX WITH A CYCLOPROPYL CARBASUGAR.
Authors
:
R. Pengelly, T. Gloster
Date
:
07 Oct 16 (Deposition) - 09 Nov 16 (Release) - 30 Nov 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.55
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Alpha-Galactosidase, Glycoside Hydrolase, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. Adamson, R. J. Pengelly, S. Shamsi Kazem Abadi, S. Chakladar, J. Draper, R. Britton, T. M. Gloster, A. J. Bennet
Structural Snapshots For Mechanism-Based Inactivation Of A Glycoside Hydrolase By Cyclopropyl Carbasugars.
Angew. Chem. Int. Ed. Engl. V. 55 14978 2016
[
close entry info
]
Hetero Components
(3, 19)
Info
All Hetero Components
1a: (1~{R},2~{S},3~{S},4~{S},6~{R})-4-... (7D8a)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
2f: 1,2-ETHANEDIOL (EDOf)
2g: 1,2-ETHANEDIOL (EDOg)
2h: 1,2-ETHANEDIOL (EDOh)
2i: 1,2-ETHANEDIOL (EDOi)
2j: 1,2-ETHANEDIOL (EDOj)
2k: 1,2-ETHANEDIOL (EDOk)
2l: 1,2-ETHANEDIOL (EDOl)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
3e: SULFATE ION (SO4e)
3f: SULFATE ION (SO4f)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
7D8
1
Ligand/Ion
(1~{R},2~{S},3~{S},4~{S},6~{R})-4-FLUORANYL-1-(HYDROXYMETHYL)BICYCLO[4.1.0]HEPTANE-2,3-DIOL
2
EDO
12
Ligand/Ion
1,2-ETHANEDIOL
3
SO4
6
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(19, 19)
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)
19: AE1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:-3 , SER A:-4 , MET A:-2 , GLY A:-5 , LYS A:111 , ASN A:290 , TRP A:291 , ASN A:292 , HOH A:806 , HOH A:917
binding site for residue SO4 A 601
02
AC2
SOFTWARE
LYS A:302 , ASP A:303 , GLU A:304 , LYS A:339
binding site for residue SO4 A 602
03
AC3
SOFTWARE
ARG A:9 , TRP A:392 , GLY A:393 , GLU A:394 , HOH A:760 , HOH A:847
binding site for residue SO4 A 603
04
AC4
SOFTWARE
GLU A:434 , LYS A:435 , THR A:436
binding site for residue SO4 A 604
05
AC5
SOFTWARE
ARG A:349 , GLU A:353 , HOH A:702 , HOH A:722 , HOH A:748
binding site for residue SO4 A 605
06
AC6
SOFTWARE
PHE A:143 , ASP A:144 , ASP A:145 , HOH A:733
binding site for residue SO4 A 606
07
AC7
SOFTWARE
SER A:-4 , TRP A:65 , TRP A:190 , TYR A:191 , ASP A:220 , ASP A:221 , TRP A:257 , LYS A:325 , ASP A:327 , PHE A:328 , CYS A:368 , ARG A:383 , ASP A:387
binding site for residue 7D8 A 607
08
AC8
SOFTWARE
ARG A:-6 , ASP A:387 , GLY A:400 , PRO A:402 , EDO A:609
binding site for residue EDO A 608
09
AC9
SOFTWARE
ARG A:-6 , TRP A:65 , THR A:88 , GLY A:400 , EDO A:608 , EDO A:612
binding site for residue EDO A 609
10
AD1
SOFTWARE
ALA A:-1 , PRO A:402 , HOH A:761 , HOH A:772 , HOH A:802 , HOH A:822
binding site for residue EDO A 610
11
AD2
SOFTWARE
LYS A:181 , HIS A:182
binding site for residue EDO A 611
12
AD3
SOFTWARE
GLN A:63 , TRP A:65 , GLY A:66 , THR A:88 , ASN A:399 , EDO A:609 , EDO A:616 , HOH A:898
binding site for residue EDO A 612
13
AD4
SOFTWARE
LYS A:357 , ARG A:496 , VAL A:512 , ASP A:514 , GLU A:519 , HOH A:701
binding site for residue EDO A 613
14
AD5
SOFTWARE
SER A:-12 , HIS A:-13 , ARG A:405 , HOH A:764 , HOH A:843 , HOH A:870
binding site for residue EDO A 614
15
AD6
SOFTWARE
LYS A:28 , ILE A:29 , HIS A:30 , LEU A:31 , HOH A:804 , HOH A:819
binding site for residue EDO A 615
16
AD7
SOFTWARE
ARG A:-6 , ILE A:81 , ASP A:82 , THR A:88 , EDO A:612 , HOH A:876 , HOH A:936
binding site for residue EDO A 616
17
AD8
SOFTWARE
PRO A:184 , ARG A:322 , ASP A:362
binding site for residue EDO A 617
18
AD9
SOFTWARE
GLY A:235
binding site for residue EDO A 618
19
AE1
SOFTWARE
ARG A:45 , ASN A:99 , GLU A:128 , TYR A:135 , HOH A:785
binding site for residue EDO A 619
[
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
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 (106 KB)
Header - Asym.Unit
Biol.Unit 1 (100 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
5M1I
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help