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.
5ERU
Asym. Unit
Info
Asym.Unit (228 KB)
Biol.Unit 1 (437 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
TERNARY COMPLEX OF GEPHE - ADP - MOLYBDENUM CLUSTER
Authors
:
V. B. Kasaragod, H. Schindelin
Date
:
15 Nov 15 (Deposition) - 04 May 16 (Release) - 11 May 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.60
Chains
:
Asym. Unit : A
Biol. Unit 1: A (2x)
Keywords
:
Molybdenum Cluster, Moco, Wco, Moco Biosynthesis, Ternary Complex, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
V. B. Kasaragod, H. Schindelin
Structural Framework For Metal Incorporation During Molybdenum Cofactor Biosynthesis.
Structure V. 24 782 2016
[
close entry info
]
Hetero Components
(8, 21)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
1c: ACETATE ION (ACTc)
1d: ACETATE ION (ACTd)
1e: ACETATE ION (ACTe)
2a: ADENOSINE-5'-DIPHOSPHATE (ADPa)
3a: CALCIUM ION (CAa)
4a: MAGNESIUM ION (MGa)
6a: MOLYBDATE ION (MOOa)
5a: MOLYBDENUM ATOM (MOa)
5b: MOLYBDENUM ATOM (MOb)
5c: MOLYBDENUM ATOM (MOc)
5d: MOLYBDENUM ATOM (MOd)
5e: MOLYBDENUM ATOM (MOe)
5f: MOLYBDENUM ATOM (MOf)
5g: MOLYBDENUM ATOM (MOg)
5h: MOLYBDENUM ATOM (MOh)
7a: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDa)
7b: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDb)
7c: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDc)
8a: PHOSPHATE ION (PO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
5
Ligand/Ion
ACETATE ION
2
ADP
1
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
3
CA
1
Ligand/Ion
CALCIUM ION
4
MG
1
Ligand/Ion
MAGNESIUM ION
5
MO
8
Ligand/Ion
MOLYBDENUM ATOM
6
MOO
1
Ligand/Ion
MOLYBDATE ION
7
MPD
3
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
8
PO4
1
Ligand/Ion
PHOSPHATE ION
[
close Hetero Component info
]
Sites
(20, 20)
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)
20: AE2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
CYS A:469
binding site for residue ACT A 801
02
AC2
SOFTWARE
ALA A:356 , HOH A:1179
binding site for residue ACT A 802
03
AC3
SOFTWARE
HOH A:1074 , HOH A:1118
binding site for residue ACT A 803
04
AC4
SOFTWARE
MPD A:808 , HOH A:916
binding site for residue ACT A 805
05
AC5
SOFTWARE
MET A:326 , ASP A:327 , PHE A:330 , PRO A:654 , ILE A:656 , MET A:731 , HOH A:939
binding site for residue MPD A 806
06
AC6
SOFTWARE
ASN A:512 , GLU A:514 , HOH A:904 , HOH A:1190 , HOH A:1252
binding site for residue MPD A 807
07
AC7
SOFTWARE
ARG A:675 , ACT A:805 , HOH A:928 , HOH A:977
binding site for residue MPD A 808
08
AC8
SOFTWARE
ADP A:810 , HOH A:932 , HOH A:984 , HOH A:1012 , HOH A:1053 , HOH A:1071 , HOH A:1121
binding site for residue CA A 809
09
AC9
SOFTWARE
SER A:505 , GLU A:509 , LEU A:510 , ILE A:522 , ASP A:524 , SER A:525 , ASN A:526 , GLY A:572 , GLY A:573 , VAL A:574 , SER A:575 , ASP A:580 , PRO A:625 , GLY A:626 , ASN A:627 , PRO A:628 , CA A:809 , MG A:821 , HOH A:932 , HOH A:972 , HOH A:1026 , HOH A:1077 , HOH A:1081 , HOH A:1111 , HOH A:1122 , HOH A:1149
binding site for residue ADP A 810
10
AD1
SOFTWARE
ARG A:564 , LYS A:619 , HOH A:910
binding site for residue PO4 A 811
11
AD2
SOFTWARE
ARG A:670 , MO A:813 , MO A:814 , MO A:816 , MO A:817 , MO A:819 , MOO A:820 , HOH A:1123
binding site for residue MO A 812
12
AD3
SOFTWARE
LEU A:605 , MO A:812 , MO A:814 , MO A:816
binding site for residue MO A 813
13
AD4
SOFTWARE
MO A:812 , MO A:813 , MO A:819 , MOO A:820 , HOH A:1219
binding site for residue MO A 814
14
AD5
SOFTWARE
MO A:817 , MO A:818 , MO A:819 , MOO A:820
binding site for residue MO A 815
15
AD6
SOFTWARE
MO A:812 , MO A:813 , MO A:817 , MO A:819 , HOH A:1123
binding site for residue MO A 816
16
AD7
SOFTWARE
LYS A:602 , MO A:812 , MO A:815 , MO A:816 , MOO A:820 , HOH A:1123
binding site for residue MO A 817
17
AD8
SOFTWARE
MO A:815 , MO A:819
binding site for residue MO A 818
18
AD9
SOFTWARE
MO A:812 , MO A:814 , MO A:815 , MO A:816 , MO A:818
binding site for residue MO A 819
19
AE1
SOFTWARE
GLY A:604 , LEU A:605 , PRO A:606 , PRO A:625 , ASN A:627 , SER A:630 , MO A:812 , MO A:814 , MO A:815 , MO A:817 , HOH A:972
binding site for residue MOO A 820
20
AE2
SOFTWARE
ASP A:580 , ADP A:810 , HOH A:932 , HOH A:1026
binding site for residue MG A 821
[
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 (228 KB)
Header - Asym.Unit
Biol.Unit 1 (437 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
5ERU
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
