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.
1YCG
Asym. Unit
Info
Asym.Unit (269 KB)
Biol.Unit 1 (133 KB)
Biol.Unit 2 (133 KB)
Biol.Unit 3 (512 KB)
Biol.Unit 4 (512 KB)
Biol.Unit 5 (260 KB)
Biol.Unit 6 (260 KB)
Biol.Unit 7 (259 KB)
Biol.Unit 8 (133 KB)
Biol.Unit 9 (133 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
X-RAY STRUCTURES OF MOORELLA THERMOACETICA FPRA. NOVEL DIIRON SITE STRUCTURE AND MECHANISTIC INSIGHTS INTO A SCAVENGING NITRIC OXIDE REDUCTASE
Authors
:
R. Silaghi-Dumitrescu, D. M. Kurtz, W. N. Lanzilotta
Date
:
22 Dec 04 (Deposition) - 19 Apr 05 (Release) - 21 Sep 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: A,B,C,D (2x)
Biol. Unit 4: A,B,C,D (2x)
Biol. Unit 5: A,B,C,D (1x)
Biol. Unit 6: A,B,C,D (1x)
Biol. Unit 7: A,B,C,D (1x)
Biol. Unit 8: B,D (1x)
Biol. Unit 9: A,C (1x)
Keywords
:
Nitric Oxide, Reductase, Diiron Site, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. Silaghi-Dumitrescu, D. M. Kurtz Jr, L. G. Ljungdahl, W. N. Lanzilotta
X-Ray Crystal Structures Of Moorella Thermoacetica Fpra. Novel Diiron Site Structure And Mechanistic Insights Into A Scavenging Nitric Oxide Reductase.
Biochemistry V. 44 6492 2005
[
close entry info
]
Hetero Components
(4, 26)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1b: 1,2-ETHANEDIOL (EDOb)
1c: 1,2-ETHANEDIOL (EDOc)
1d: 1,2-ETHANEDIOL (EDOd)
2a: MU-OXO-DIIRON (FEOa)
2b: MU-OXO-DIIRON (FEOb)
2c: MU-OXO-DIIRON (FEOc)
2d: MU-OXO-DIIRON (FEOd)
3a: FLAVIN MONONUCLEOTIDE (FMNa)
3b: FLAVIN MONONUCLEOTIDE (FMNb)
3c: FLAVIN MONONUCLEOTIDE (FMNc)
3d: FLAVIN MONONUCLEOTIDE (FMNd)
4a: ZINC ION (ZNa)
4b: ZINC ION (ZNb)
4c: ZINC ION (ZNc)
4d: ZINC ION (ZNd)
4e: ZINC ION (ZNe)
4f: ZINC ION (ZNf)
4g: ZINC ION (ZNg)
4h: ZINC ION (ZNh)
4i: ZINC ION (ZNi)
4j: ZINC ION (ZNj)
4k: ZINC ION (ZNk)
4l: ZINC ION (ZNl)
4m: ZINC ION (ZNm)
4n: ZINC ION (ZNn)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
4
Ligand/Ion
1,2-ETHANEDIOL
2
FEO
4
Ligand/Ion
MU-OXO-DIIRON
3
FMN
4
Ligand/Ion
FLAVIN MONONUCLEOTIDE
4
ZN
14
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(26, 26)
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)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER A:2 , GLU A:60 , HIS C:271 , ASP C:275 , ZN C:422
BINDING SITE FOR RESIDUE ZN A 401
02
AC2
SOFTWARE
HIS A:271 , ASP A:275 , SER C:2 , GLU C:60 , ZN C:421
BINDING SITE FOR RESIDUE ZN A 402
03
AC3
SOFTWARE
HIS A:118 , HOH A:729 , GLU D:388 , HOH D:761
BINDING SITE FOR RESIDUE ZN A 403
04
AC4
SOFTWARE
GLU A:59 , HOH A:730 , HOH A:731 , HOH A:732
BINDING SITE FOR RESIDUE ZN A 404
05
AC5
SOFTWARE
SER B:2 , GLU B:60 , HIS D:271 , ASP D:275 , ZN D:432
BINDING SITE FOR RESIDUE ZN B 411
06
AC6
SOFTWARE
HIS B:271 , ASP B:275 , SER D:2 , GLU D:60 , ZN D:431
BINDING SITE FOR RESIDUE ZN B 412
07
AC7
SOFTWARE
ASP B:120 , HOH B:731 , HOH B:732 , HOH B:733 , HOH B:734
BINDING SITE FOR RESIDUE ZN B 413
08
AC8
SOFTWARE
GLU B:55 , GLU B:59 , HOH B:735 , HOH B:736 , HOH B:737
BINDING SITE FOR RESIDUE ZN B 414
09
AC9
SOFTWARE
HIS A:271 , ASP A:275 , ZN A:402 , SER C:2 , GLU C:60
BINDING SITE FOR RESIDUE ZN C 421
10
BC1
SOFTWARE
SER A:2 , GLU A:60 , ZN A:401 , HIS C:271 , ASP C:275
BINDING SITE FOR RESIDUE ZN C 422
11
BC2
SOFTWARE
PRO C:56 , GLU C:59 , HOH C:728 , HOH C:758 , HOH C:759 , HOH C:760 , HOH C:761
BINDING SITE FOR RESIDUE ZN C 423
12
BC3
SOFTWARE
HIS B:271 , ASP B:275 , ZN B:412 , SER D:2 , GLU D:60
BINDING SITE FOR RESIDUE ZN D 431
13
BC4
SOFTWARE
SER B:2 , GLU B:60 , ZN B:411 , HIS D:271 , ASP D:275
BINDING SITE FOR RESIDUE ZN D 432
14
BC5
SOFTWARE
GLU D:55 , HOH D:763 , HOH D:764 , HOH D:765 , HOH D:766
BINDING SITE FOR RESIDUE ZN D 433
15
BC6
SOFTWARE
HIS A:81 , GLU A:83 , ASP A:85 , HIS A:86 , HIS A:148 , ASP A:167 , HIS A:228 , EDO A:602
BINDING SITE FOR RESIDUE FEO A 501
16
BC7
SOFTWARE
PHE A:24 , HIS A:25 , GLU A:83 , ASP A:85 , HIS A:148 , ASP A:167 , HIS A:228 , FEO A:501
BINDING SITE FOR RESIDUE EDO A 602
17
BC8
SOFTWARE
THR A:261 , MET A:262 , TRP A:263 , LEU A:264 , SER A:265 , THR A:266 , PRO A:312 , THR A:313 , ILE A:314 , ASN A:315 , ASN A:316 , ALA A:344 , TYR A:345 , GLY A:346 , TRP A:347 , GLY A:348 , GLY A:349 , TRP A:376 , HOH A:715 , HOH A:716 , HIS B:25 , GLU B:83 , HIS B:148 , TRP B:149
BINDING SITE FOR RESIDUE FMN A 701
18
BC9
SOFTWARE
HIS B:81 , GLU B:83 , ASP B:85 , HIS B:86 , HIS B:148 , ASP B:167 , HIS B:228 , EDO B:612
BINDING SITE FOR RESIDUE FEO B 511
19
CC1
SOFTWARE
PHE B:24 , HIS B:25 , GLU B:83 , ASP B:85 , HIS B:148 , ASP B:167 , HIS B:228 , FEO B:511
BINDING SITE FOR RESIDUE EDO B 612
20
CC2
SOFTWARE
HIS A:25 , GLU A:83 , HIS A:148 , TRP A:149 , HOH A:728 , THR B:261 , MET B:262 , TRP B:263 , LEU B:264 , SER B:265 , THR B:266 , PRO B:312 , THR B:313 , ILE B:314 , ASN B:315 , ASN B:316 , ALA B:344 , TYR B:345 , GLY B:346 , TRP B:347 , GLY B:348 , GLY B:349 , TRP B:376 , HOH B:730
BINDING SITE FOR RESIDUE FMN B 711
21
CC3
SOFTWARE
HIS C:81 , GLU C:83 , ASP C:85 , HIS C:86 , HIS C:148 , ASP C:167 , HIS C:228 , EDO C:622
BINDING SITE FOR RESIDUE FEO C 521
22
CC4
SOFTWARE
PHE C:24 , HIS C:25 , GLU C:83 , ASP C:85 , HIS C:148 , FEO C:521
BINDING SITE FOR RESIDUE EDO C 622
23
CC5
SOFTWARE
THR C:261 , MET C:262 , TRP C:263 , LEU C:264 , SER C:265 , THR C:266 , PRO C:312 , THR C:313 , ILE C:314 , ASN C:315 , ASN C:316 , ALA C:344 , TYR C:345 , GLY C:346 , TRP C:347 , GLY C:348 , GLY C:349 , TRP C:376 , HOH C:748 , HIS D:25 , GLU D:83 , HIS D:148 , TRP D:149 , HOH D:758
BINDING SITE FOR RESIDUE FMN C 721
24
CC6
SOFTWARE
HIS D:81 , GLU D:83 , ASP D:85 , HIS D:86 , HIS D:148 , ASP D:167 , HIS D:228 , EDO D:632
BINDING SITE FOR RESIDUE FEO D 531
25
CC7
SOFTWARE
TRP C:263 , PHE D:24 , HIS D:25 , GLU D:83 , ASP D:85 , HIS D:148 , HIS D:228 , FEO D:531
BINDING SITE FOR RESIDUE EDO D 632
26
CC8
SOFTWARE
HIS C:25 , GLU C:83 , HIS C:148 , TRP C:149 , THR D:261 , MET D:262 , TRP D:263 , LEU D:264 , SER D:265 , THR D:266 , PRO D:312 , THR D:313 , ILE D:314 , ASN D:315 , ASN D:316 , ALA D:344 , TYR D:345 , GLY D:346 , TRP D:347 , GLY D:348 , GLY D:349 , TRP D:376 , HOH D:759 , HOH D:760
BINDING SITE FOR RESIDUE FMN D 731
[
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
(1, 4)
Info
All PROSITE Patterns/Profiles
1: FLAVODOXIN_LIKE (A:255-394,B:255-394,C:255-394,D:25...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
FLAVODOXIN_LIKE
PS50902
Flavodoxin-like domain profile.
FPRA_MOOTA
255-394
4
A:255-394
B:255-394
C:255-394
D:255-394
[
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
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1ycga2 (A:2-250)
1b: SCOP_d1ycgb2 (B:2-250)
1c: SCOP_d1ycgc2 (C:2-250)
1d: SCOP_d1ycgd2 (D:2-250)
2a: SCOP_d1ycga1 (A:251-399)
2b: SCOP_d1ycgb1 (B:251-399)
2c: SCOP_d1ycgc1 (C:251-399)
2d: SCOP_d1ycgd1 (D:251-399)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Metallo-hydrolase/oxidoreductase
(184)
Superfamily
:
Metallo-hydrolase/oxidoreductase
(184)
Family
:
ROO N-terminal domain-like
(9)
Protein domain
:
Nitric oxide reductase N-terminal domain
(4)
Moorella thermoacetica [TaxId: 1525]
(3)
1a
d1ycga2
A:2-250
1b
d1ycgb2
B:2-250
1c
d1ycgc2
C:2-250
1d
d1ycgd2
D:2-250
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Flavodoxin-like
(1057)
Superfamily
:
Flavoproteins
(208)
Family
:
Flavodoxin-related
(81)
Protein domain
:
Nitric oxide reductase C-terminal domain
(4)
Moorella thermoacetica [TaxId: 1525]
(3)
2a
d1ycga1
A:251-399
2b
d1ycgb1
B:251-399
2c
d1ycgc1
C:251-399
2d
d1ycgd1
D:251-399
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1ycgA02 (A:254-396)
1b: CATH_1ycgB02 (B:254-396)
1c: CATH_1ycgC02 (C:254-396)
1d: CATH_1ycgD02 (D:254-396)
2a: CATH_1ycgA01 (A:2-248)
2b: CATH_1ycgB01 (B:2-248)
2c: CATH_1ycgC01 (C:2-248)
2d: CATH_1ycgD01 (D:2-248)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.360, no name defined]
(150)
Moorella thermoacetica. Organism_taxid: 1525.
(2)
1a
1ycgA02
A:254-396
1b
1ycgB02
B:254-396
1c
1ycgC02
C:254-396
1d
1ycgD02
D:254-396
Architecture
:
4-Layer Sandwich
(459)
Topology
:
Metallo-beta-lactamase; Chain A
(92)
Homologous Superfamily
:
Metallo-beta-lactamase, chain A
(92)
Moorella thermoacetica. Organism_taxid: 1525.
(2)
2a
1ycgA01
A:2-248
2b
1ycgB01
B:2-248
2c
1ycgC01
C:2-248
2d
1ycgD01
D:2-248
[
close CATH info
]
Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_Flavodoxin_1_1ycgD01 (D:257-390)
1b: PFAM_Flavodoxin_1_1ycgD02 (D:257-390)
1c: PFAM_Flavodoxin_1_1ycgD03 (D:257-390)
1d: PFAM_Flavodoxin_1_1ycgD04 (D:257-390)
2a: PFAM_Lactamase_B_1ycgD05 (D:32-241)
2b: PFAM_Lactamase_B_1ycgD06 (D:32-241)
2c: PFAM_Lactamase_B_1ycgD07 (D:32-241)
2d: PFAM_Lactamase_B_1ycgD08 (D:32-241)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Flavoprotein
(71)
Family
:
Flavodoxin_1
(23)
Moorella thermoacetica (strain ATCC 39073)
(2)
1a
Flavodoxin_1-1ycgD01
D:257-390
1b
Flavodoxin_1-1ycgD02
D:257-390
1c
Flavodoxin_1-1ycgD03
D:257-390
1d
Flavodoxin_1-1ycgD04
D:257-390
Clan
:
Metallo-HOrase
(67)
Family
:
Lactamase_B
(53)
Moorella thermoacetica (strain ATCC 39073)
(2)
2a
Lactamase_B-1ycgD05
D:32-241
2b
Lactamase_B-1ycgD06
D:32-241
2c
Lactamase_B-1ycgD07
D:32-241
2d
Lactamase_B-1ycgD08
D:32-241
[
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 (269 KB)
Header - Asym.Unit
Biol.Unit 1 (133 KB)
Header - Biol.Unit 1
Biol.Unit 2 (133 KB)
Header - Biol.Unit 2
Biol.Unit 3 (512 KB)
Header - Biol.Unit 3
Biol.Unit 4 (512 KB)
Header - Biol.Unit 4
Biol.Unit 5 (260 KB)
Header - Biol.Unit 5
Biol.Unit 6 (260 KB)
Header - Biol.Unit 6
Biol.Unit 7 (259 KB)
Header - Biol.Unit 7
Biol.Unit 8 (133 KB)
Header - Biol.Unit 8
Biol.Unit 9 (133 KB)
Header - Biol.Unit 9
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
1YCG
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
