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.
1KYQ
Biol. Unit 2
Info
Asym.Unit (155 KB)
Biol.Unit 1 (100 KB)
Biol.Unit 2 (99 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
MET8P: A BIFUNCTIONAL NAD-DEPENDENT DEHYDROGENASE AND FERROCHELATASE INVOLVED IN SIROHEME SYNTHESIS.
Authors
:
H. L. Schubert, E. Raux, A. A. Brindley, K. S. Wilson, C. P. Hill, M. J. Warren
Date
:
05 Feb 02 (Deposition) - 08 May 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C (2x)
Keywords
:
Homodimer, Oxidoreductase, Lyase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. L. Schubert, E. Raux, A. A. Brindley, H. K. Leech, K. S. Wilson, C. P. Hill, M. J. Warren
The Structure Of Saccharomyces Cerevisiae Met8P, A Bifunctional Dehydrogenase And Ferrochelatase.
Embo J. V. 21 2068 2002
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 14)
Info
All Hetero Components
1a: SELENOMETHIONINE (MSEa)
1b: SELENOMETHIONINE (MSEb)
1c: SELENOMETHIONINE (MSEc)
1d: SELENOMETHIONINE (MSEd)
1e: SELENOMETHIONINE (MSEe)
1f: SELENOMETHIONINE (MSEf)
1g: SELENOMETHIONINE (MSEg)
1h: SELENOMETHIONINE (MSEh)
1i: SELENOMETHIONINE (MSEi)
1j: SELENOMETHIONINE (MSEj)
1k: SELENOMETHIONINE (MSEk)
1l: SELENOMETHIONINE (MSEl)
1m: SELENOMETHIONINE (MSEm)
1n: SELENOMETHIONINE (MSEn)
1o: SELENOMETHIONINE (MSEo)
1p: SELENOMETHIONINE (MSEp)
1q: SELENOMETHIONINE (MSEq)
1r: SELENOMETHIONINE (MSEr)
2a: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADa)
2b: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADb)
2c: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NADc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MSE
12
Mod. Amino Acid
SELENOMETHIONINE
2
NAD
2
Ligand/Ion
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
[
close Hetero Component info
]
Sites
(1, 1)
Info
All Sites
1: AC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC3
SOFTWARE
ILE C:19 , GLY C:20 , GLY C:21 , GLY C:22 , GLU C:23 , VAL C:24 , VAL C:42 , SER C:43 , PRO C:44 , ASP C:45 , ASP C:92 , PHE C:93 , CYS C:113 , ILE C:114 , ALA C:140 , ASP C:141 , HOH C:809 , HOH C:811 , HOH C:812 , HOH C:877 , HOH C:925
BINDING SITE FOR RESIDUE NAD C 802
[
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
(2, 6)
Info
All SCOP Domains
1a: SCOP_d1kyqa1 (A:1-150)
1b: SCOP_d1kyqb1 (B:1-150)
1c: SCOP_d1kyqc1 (C:1-150)
2a: SCOP_d1kyqa2 (A:151-273)
2b: SCOP_d1kyqb2 (B:151-273)
2c: SCOP_d1kyqc2 (C:151-273)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
Siroheme synthase N-terminal domain-like
(4)
Protein domain
:
Bifunctional dehydrogenase/ferrochelatase Met8p, N-terminal domain
(1)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(1)
1a
d1kyqa1
A:1-150
1b
d1kyqb1
B:1-150
1c
d1kyqc1
C:1-150
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
Siroheme synthase middle domains-like
(4)
Superfamily
:
Siroheme synthase middle domains-like
(4)
Family
:
Siroheme synthase middle domains-like
(4)
Protein domain
:
Bifunctional dehydrogenase/ferrochelatase Met8p, dimerisation and C-terminal domains
(1)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(1)
2a
d1kyqa2
A:151-273
2b
d1kyqb2
B:151-273
2c
d1kyqc2
C:151-273
[
close SCOP info
]
CATH Domains
(3, 9)
Info
all CATH domains
1a: CATH_1kyqA02 (A:151-187)
1b: CATH_1kyqB02 (B:151-187)
1c: CATH_1kyqC02 (C:151-187)
2a: CATH_1kyqB01 (B:2-150)
2b: CATH_1kyqA01 (A:2-150)
2c: CATH_1kyqC01 (C:2-150)
3a: CATH_1kyqA03 (A:190-273)
3b: CATH_1kyqB03 (B:190-273)
3c: CATH_1kyqC03 (C:189-273)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Double Stranded RNA Binding Domain
(204)
Homologous Superfamily
:
Siroheme synthase; domain 2
(6)
Baker's yeast (Saccharomyces cerevisiae)
(1)
1a
1kyqA02
A:151-187
1b
1kyqB02
B:151-187
1c
1kyqC02
C:151-187
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Baker's yeast (Saccharomyces cerevisiae)
(13)
2a
1kyqB01
B:2-150
2b
1kyqA01
A:2-150
2c
1kyqC01
C:2-150
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Siro heme synthase C-terminal domain-like
(1)
Homologous Superfamily
:
Siroheme synthase; domain 3
(1)
Baker's yeast (Saccharomyces cerevisiae)
(1)
3a
1kyqA03
A:190-273
3b
1kyqB03
B:190-273
3c
1kyqC03
C:189-273
[
close CATH info
]
Pfam Domains
(1, 3)
Info
all PFAM domains
1a: PFAM_NAD_binding_7_1kyqC01 (C:7-152)
1b: PFAM_NAD_binding_7_1kyqC02 (C:7-152)
1c: PFAM_NAD_binding_7_1kyqC03 (C:7-152)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
NADP_Rossmann
(1239)
Family
:
NAD_binding_7
(3)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(1)
1a
NAD_binding_7-1kyqC01
C:7-152
1b
NAD_binding_7-1kyqC02
C:7-152
1c
NAD_binding_7-1kyqC03
C:7-152
[
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 C
Asymmetric Unit 1
Asymmetric Unit 2
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 (155 KB)
Header - Asym.Unit
Biol.Unit 1 (100 KB)
Header - Biol.Unit 1
Biol.Unit 2 (99 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
1KYQ
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help