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.
2PP8
Asym. Unit
Info
Asym.Unit (357 KB)
Biol.Unit 1 (351 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
FORMATE BOUND TO OXIDIZED WILD TYPE AFNIR
Authors
:
E. I. Tocheva, L. D. Eltis, M. E. P. Murphy
Date
:
28 Apr 07 (Deposition) - 01 Apr 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.50
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Nitrite Reductase, Denitrification, Bacteria, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. I. Tocheva, L. D. Eltis, M. E. Murphy
Conserved Active Site Residues Limit Inhibition Of A Copper-Containing Nitrite Reductase By Small Molecules.
Biochemistry V. 47 4452 2008
[
close entry info
]
Hetero Components
(5, 18)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
1c: ACETATE ION (ACTc)
1d: ACETATE ION (ACTd)
1e: ACETATE ION (ACTe)
1f: ACETATE ION (ACTf)
1g: ACETATE ION (ACTg)
1h: ACETATE ION (ACTh)
2a: COPPER (I) ION (CU1a)
2b: COPPER (I) ION (CU1b)
2c: COPPER (I) ION (CU1c)
3a: COPPER (II) ION (CUa)
3b: COPPER (II) ION (CUb)
3c: COPPER (II) ION (CUc)
4a: FORMIC ACID (FMTa)
4b: FORMIC ACID (FMTb)
4c: FORMIC ACID (FMTc)
5a: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,... (TRSa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
8
Ligand/Ion
ACETATE ION
3
CU
3
Ligand/Ion
COPPER (II) ION
2
CU1
3
Ligand/Ion
COPPER (I) ION
4
FMT
3
Ligand/Ion
FORMIC ACID
5
TRS
1
Ligand/Ion
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
[
close Hetero Component info
]
Sites
(18, 18)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:95 , CYS A:136 , HIS A:145 , MET A:150
BINDING SITE FOR RESIDUE CU1 A 501
02
AC2
SOFTWARE
HIS A:100 , HIS A:135 , HIS B:306
BINDING SITE FOR RESIDUE CU A 502
03
AC3
SOFTWARE
HIS B:95 , CYS B:136 , HIS B:145 , MET B:150
BINDING SITE FOR RESIDUE CU1 B 501
04
AC4
SOFTWARE
HIS B:100 , HIS B:135 , HIS C:306
BINDING SITE FOR RESIDUE CU B 502
05
AC5
SOFTWARE
HIS C:95 , CYS C:136 , HIS C:145 , MET C:150
BINDING SITE FOR RESIDUE CU1 C 501
06
AC6
SOFTWARE
HIS A:306 , HIS C:100 , HIS C:135
BINDING SITE FOR RESIDUE CU C 502
07
AC7
SOFTWARE
THR B:228 , GLY B:229 , ILE B:300 , HIS B:319
BINDING SITE FOR RESIDUE ACT B 1503
08
AC8
SOFTWARE
HOH A:1545 , ASP B:173 , GLY B:238 , GLU B:239 , LYS B:240 , HOH B:1583
BINDING SITE FOR RESIDUE ACT B 1504
09
AC9
SOFTWARE
GLY B:140 , MET B:141 , PRO B:143 , TRP B:144 , MET B:210 , GLU C:313
BINDING SITE FOR RESIDUE ACT B 1505
10
BC1
SOFTWARE
PHE B:282 , PHE C:282 , HOH C:1512 , HOH C:1518 , HOH C:1643 , HOH C:1664
BINDING SITE FOR RESIDUE ACT C 1506
11
BC2
SOFTWARE
HIS C:60 , TYR C:184 , PRO C:186 , THR C:206 , HOH C:1538 , HOH C:1623
BINDING SITE FOR RESIDUE ACT C 1507
12
BC3
SOFTWARE
GLU A:313 , GLY C:140 , MET C:141 , PRO C:143 , TRP C:144
BINDING SITE FOR RESIDUE ACT C 1508
13
BC4
SOFTWARE
THR C:228 , GLY C:229 , HIS C:319 , LYS C:321
BINDING SITE FOR RESIDUE ACT C 1509
14
BC5
SOFTWARE
GLY A:140 , MET A:141 , PRO A:143 , TRP A:144 , TYR A:203 , MET A:210 , GLU B:313 , GLU B:325
BINDING SITE FOR RESIDUE ACT A 1510
15
BC6
SOFTWARE
THR A:212 , LEU A:213 , THR A:214 , HOH A:1666 , HOH A:1706 , HOH A:1713 , THR B:212 , LEU B:213 , THR B:214 , THR C:212 , LEU C:213 , THR C:214
BINDING SITE FOR RESIDUE TRS A 1501
16
BC7
SOFTWARE
ASP A:98 , HIS A:100 , HIS A:135 , HOH A:1910 , ILE B:257 , HIS B:306 , LEU B:308
BINDING SITE FOR RESIDUE FMT A 401
17
BC8
SOFTWARE
ASP B:98 , HIS B:100 , HIS B:135 , ALA B:137 , HOH B:1817 , HOH B:1880 , ILE C:257 , HIS C:306
BINDING SITE FOR RESIDUE FMT B 401
18
BC9
SOFTWARE
ILE A:257 , HIS A:306 , ASP C:98 , HIS C:100 , HIS C:135 , ALA C:137 , HOH C:1742 , HOH C:1832
BINDING SITE FOR RESIDUE FMT C 401
[
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, 6)
Info
All SCOP Domains
1a: SCOP_d2pp8a1 (A:4-166)
1b: SCOP_d2pp8a2 (A:167-339)
1c: SCOP_d2pp8b1 (B:4-166)
1d: SCOP_d2pp8b2 (B:167-339)
1e: SCOP_d2pp8c1 (C:4-166)
1f: SCOP_d2pp8c2 (C:167-339)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Cupredoxin-like
(545)
Superfamily
:
Cupredoxins
(543)
Family
:
Multidomain cupredoxins
(146)
Protein domain
:
Nitrite reductase, NIR
(79)
Alcaligenes faecalis, strain s-6 [TaxId: 511]
(31)
1a
d2pp8a1
A:4-166
1b
d2pp8a2
A:167-339
1c
d2pp8b1
B:4-166
1d
d2pp8b2
B:167-339
1e
d2pp8c1
C:4-166
1f
d2pp8c2
C:167-339
[
close SCOP info
]
CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_2pp8A01 (A:11-158)
1b: CATH_2pp8B01 (B:11-158)
1c: CATH_2pp8C01 (C:11-158)
1d: CATH_2pp8A02 (A:159-325)
1e: CATH_2pp8B02 (B:159-325)
1f: CATH_2pp8C02 (C:159-325)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Cupredoxins - blue copper proteins
(420)
Alcaligenes faecalis. Organism_taxid: 511. Strain: s-6.
(24)
1a
2pp8A01
A:11-158
1b
2pp8B01
B:11-158
1c
2pp8C01
C:11-158
1d
2pp8A02
A:159-325
1e
2pp8B02
B:159-325
1f
2pp8C02
C:159-325
[
close CATH info
]
Pfam Domains
(2, 6)
Info
all PFAM domains
1a: PFAM_Cu_oxidase_2pp8C01 (C:174-326)
1b: PFAM_Cu_oxidase_2pp8C02 (C:174-326)
1c: PFAM_Cu_oxidase_2pp8C03 (C:174-326)
2a: PFAM_Cu_oxidase_3_2pp8C04 (C:44-161)
2b: PFAM_Cu_oxidase_3_2pp8C05 (C:44-161)
2c: PFAM_Cu_oxidase_3_2pp8C06 (C:44-161)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
CU_oxidase
(192)
Family
:
Cu-oxidase
(74)
Alcaligenes faecalis
(18)
1a
Cu-oxidase-2pp8C01
C:174-326
1b
Cu-oxidase-2pp8C02
C:174-326
1c
Cu-oxidase-2pp8C03
C:174-326
Family
:
Cu-oxidase_3
(79)
Alcaligenes faecalis
(18)
2a
Cu-oxidase_3-2pp8C04
C:44-161
2b
Cu-oxidase_3-2pp8C05
C:44-161
2c
Cu-oxidase_3-2pp8C06
C:44-161
[
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
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 (357 KB)
Header - Asym.Unit
Biol.Unit 1 (351 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
2PP8
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
