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.
3HNI
Asym. Unit
Info
Asym.Unit (153 KB)
Biol.Unit 1 (73 KB)
Biol.Unit 2 (73 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 THE ZN-INDUCED TETRAMER OF THE ENGINEERED CYT CB562 VARIANT RIDC-1
Authors
:
E. N. Salgado, R. A. Lewis, J. Brodin, F. A. Tezcan
Date
:
31 May 09 (Deposition) - 09 Feb 10 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.35
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Keywords
:
Electron Transport, Metal Binding Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. N. Salgado, X. I. Ambroggio, J. D. Brodin, R. A. Lewis, B. Kuhlman, F. A. Tezcan
Metal Templated Design Of Protein Interfaces.
Proc. Natl. Acad. Sci. Usa V. 107 1827 2010
[
close entry info
]
Hetero Components
(2, 16)
Info
All Hetero Components
1a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
1b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
1c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
1d: PROTOPORPHYRIN IX CONTAINING FE (HEMd)
1e: PROTOPORPHYRIN IX CONTAINING FE (HEMe)
1f: PROTOPORPHYRIN IX CONTAINING FE (HEMf)
1g: PROTOPORPHYRIN IX CONTAINING FE (HEMg)
1h: PROTOPORPHYRIN IX CONTAINING FE (HEMh)
2a: ZINC ION (ZNa)
2b: ZINC ION (ZNb)
2c: ZINC ION (ZNc)
2d: ZINC ION (ZNd)
2e: ZINC ION (ZNe)
2f: ZINC ION (ZNf)
2g: ZINC ION (ZNg)
2h: ZINC ION (ZNh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
HEM
8
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
2
ZN
8
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(16, 16)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LEU A:3 , GLU A:4 , MET A:7 , GLU A:8 , MET A:33 , PRO A:45 , PRO A:46 , PHE A:61 , PHE A:65 , CYS A:98 , CYS A:101 , HIS A:102 , TYR A:105 , ARG A:106 , ASP D:2 , GLU D:4 , GLU D:49
BINDING SITE FOR RESIDUE HEM A 150
02
AC2
SOFTWARE
HIS A:73 , HIS A:77 , ASP C:74 , HIS D:63
BINDING SITE FOR RESIDUE ZN A 107
03
AC3
SOFTWARE
GLU B:4 , MET B:7 , GLU B:8 , ASN B:11 , PRO B:45 , PRO B:46 , PHE B:61 , PHE B:65 , LEU B:68 , LEU B:94 , CYS B:98 , CYS B:101 , HIS B:102 , ARG B:106 , LYS D:47 , ARG D:106
BINDING SITE FOR RESIDUE HEM B 150
04
AC4
SOFTWARE
HIS B:73 , HIS B:77 , HIS C:63 , ASP D:74
BINDING SITE FOR RESIDUE ZN B 107
05
AC5
SOFTWARE
GLU C:4 , MET C:7 , ASN C:11 , PRO C:45 , PHE C:61 , CYS C:98 , CYS C:101 , HIS C:102 , ARG C:106 , GLN F:103 , ASP H:5
BINDING SITE FOR RESIDUE HEM C 150
06
AC6
SOFTWARE
ASP A:74 , HIS B:63 , HIS C:73 , HIS C:77
BINDING SITE FOR RESIDUE ZN C 107
07
AC7
SOFTWARE
GLU B:8 , ASN B:11 , LYS B:15 , GLU D:4 , MET D:7 , LEU D:14 , PRO D:45 , PRO D:46 , PHE D:61 , PHE D:65 , CYS D:98 , CYS D:101 , HIS D:102 , ARG D:106
BINDING SITE FOR RESIDUE HEM D 150
08
AC8
SOFTWARE
HIS A:63 , ASP B:74 , HIS D:73 , HIS D:77
BINDING SITE FOR RESIDUE ZN D 107
09
AC9
SOFTWARE
GLU E:4 , MET E:7 , GLU E:8 , PRO E:45 , PHE E:61 , PHE E:65 , LEU E:68 , CYS E:98 , CYS E:101 , HIS E:102 , ARG E:106 , GLU F:49
BINDING SITE FOR RESIDUE HEM E 150
10
BC1
SOFTWARE
HIS E:73 , HIS E:77 , HIS F:63 , ASP G:74
BINDING SITE FOR RESIDUE ZN E 107
11
BC2
SOFTWARE
LEU F:3 , GLU F:4 , MET F:7 , ASN F:11 , LEU F:14 , PRO F:45 , PRO F:46 , PHE F:61 , PHE F:65 , LEU F:68 , CYS F:98 , CYS F:101 , HIS F:102 , ARG F:106 , HOH F:137 , GLU H:8 , LYS H:15
BINDING SITE FOR RESIDUE HEM F 150
12
BC3
SOFTWARE
HIS E:63 , HIS F:73 , HIS F:77 , ASP H:74
BINDING SITE FOR RESIDUE ZN F 107
13
BC4
SOFTWARE
ASP B:5 , GLN D:103 , GLU G:4 , MET G:7 , ASN G:11 , PRO G:45 , PRO G:46 , PHE G:61 , PHE G:65 , CYS G:98 , CYS G:101 , HIS G:102 , ARG G:106
BINDING SITE FOR RESIDUE HEM G 150
14
BC5
SOFTWARE
ASP E:74 , HIS G:73 , HIS G:77 , HIS H:63
BINDING SITE FOR RESIDUE ZN G 107
15
BC6
SOFTWARE
LYS F:47 , GLU H:4 , MET H:7 , GLU H:8 , ASN H:11 , PRO H:45 , PRO H:46 , PHE H:61 , LEU H:68 , LEU H:94 , CYS H:98 , CYS H:101 , HIS H:102 , ARG H:106
BINDING SITE FOR RESIDUE HEM H 150
16
BC7
SOFTWARE
ASP F:74 , HIS G:63 , HIS H:73 , HIS H:77
BINDING SITE FOR RESIDUE ZN H 107
[
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
(1, 8)
Info
All SCOP Domains
1a: SCOP_d3hnia_ (A:)
1b: SCOP_d3hnib_ (B:)
1c: SCOP_d3hnic_ (C:)
1d: SCOP_d3hnid_ (D:)
1e: SCOP_d3hnie_ (E:)
1f: SCOP_d3hnif_ (F:)
1g: SCOP_d3hnig_ (G:)
1h: SCOP_d3hnih_ (H:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Four-helical up-and-down bundle
(308)
Superfamily
:
Cytochromes
(82)
Family
:
Cytochrome b562
(38)
Protein domain
:
automated matches
(32)
Escherichia coli [TaxId: 562]
(31)
1a
d3hnia_
A:
1b
d3hnib_
B:
1c
d3hnic_
C:
1d
d3hnid_
D:
1e
d3hnie_
E:
1f
d3hnif_
F:
1g
d3hnig_
G:
1h
d3hnih_
H:
[
close SCOP info
]
CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_3hniA00 (A:1-106)
1b: CATH_3hniB00 (B:1-106)
1c: CATH_3hniC00 (C:1-106)
1d: CATH_3hniD00 (D:1-106)
1e: CATH_3hniE00 (E:1-106)
1f: CATH_3hniF00 (F:1-106)
1g: CATH_3hniG00 (G:1-106)
1h: CATH_3hniH00 (H:1-106)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Four Helix Bundle (Hemerythrin (Met), subunit A)
(300)
Homologous Superfamily
:
[code=1.20.120.10, no name defined]
(45)
Escherichia coli. Organism_taxid: 562.
(13)
1a
3hniA00
A:1-106
1b
3hniB00
B:1-106
1c
3hniC00
C:1-106
1d
3hniD00
D:1-106
1e
3hniE00
E:1-106
1f
3hniF00
F:1-106
1g
3hniG00
G:1-106
1h
3hniH00
H:1-106
[
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
Chain E
Chain F
Chain G
Chain H
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 (153 KB)
Header - Asym.Unit
Biol.Unit 1 (73 KB)
Header - Biol.Unit 1
Biol.Unit 2 (73 KB)
Header - Biol.Unit 2
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
3HNI
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
