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.
3MZ9
Asym. Unit
Info
Asym.Unit (186 KB)
Biol.Unit 1 (94 KB)
Biol.Unit 2 (90 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 STRUCTURE OF NIKA IN COMPLEX WITH HBED
Authors
:
C. Cavazza, C. Bochot, P. Rousselot-Pailley, P. Carpentier, M. V. Cher L. Martin, C. Marchi-Delapierre, J. C. Fontecilla-Camps, S. Menage
Date
:
12 May 10 (Deposition) - 09 Feb 11 (Release) - 09 Feb 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Protein-Boundiron Complex, Transport Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. Cavazza, C. Bochot, P. Rousselot-Pailley, P. Carpentier, M. V. Cherrier, L. Martin, C. Marchi-Delapierre, J. C. Fontecilla-Camps, S. Menage
Crystallographic Snapshots Of The Reaction Of Aromatic C-H With O(2) Catalysed By A Protein-Bound Iron Complex
Nat. Chem. V. 2 1069 2010
[
close entry info
]
Hetero Components
(7, 32)
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: 2-[2-[CARBOXYMETHYL-[(2-HYDROXYPHE... (BHNa)
2b: 2-[2-[CARBOXYMETHYL-[(2-HYDROXYPHE... (BHNb)
3a: CHLORIDE ION (CLa)
3b: CHLORIDE ION (CLb)
3c: CHLORIDE ION (CLc)
3d: CHLORIDE ION (CLd)
4a: DITHIANE DIOL (DTDa)
4b: DITHIANE DIOL (DTDb)
5a: FE (III) ION (FEa)
5b: FE (III) ION (FEb)
6a: GLYCEROL (GOLa)
6b: GLYCEROL (GOLb)
6c: GLYCEROL (GOLc)
6d: GLYCEROL (GOLd)
6e: GLYCEROL (GOLe)
6f: GLYCEROL (GOLf)
6g: GLYCEROL (GOLg)
6h: GLYCEROL (GOLh)
6i: GLYCEROL (GOLi)
6j: GLYCEROL (GOLj)
6k: GLYCEROL (GOLk)
6l: GLYCEROL (GOLl)
6m: GLYCEROL (GOLm)
7a: SULFATE ION (SO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
8
Ligand/Ion
ACETATE ION
2
BHN
2
Ligand/Ion
2-[2-[CARBOXYMETHYL-[(2-HYDROXYPHENYL)METHYL]AMINO]ETHYL-[(2-HYDROXYPHENYL)METHYL]AMINO]ETHANOIC ACID
3
CL
4
Ligand/Ion
CHLORIDE ION
4
DTD
2
Ligand/Ion
DITHIANE DIOL
5
FE
2
Ligand/Ion
FE (III) ION
6
GOL
13
Ligand/Ion
GLYCEROL
7
SO4
1
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(32, 32)
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)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
BHN A:504
BINDING SITE FOR RESIDUE FE A 503
02
AC2
SOFTWARE
TYR A:22 , THR A:23 , MET A:27 , TRP A:100 , ARG A:137 , TRP A:398 , HIS A:416 , THR A:490 , FE A:503 , HOH A:597 , HOH A:691 , HOH A:867 , HOH A:901 , HOH A:927
BINDING SITE FOR RESIDUE BHN A 504
03
AC3
SOFTWARE
TRP A:10 , PRO A:11 , ARG A:205 , GLY A:219 , ASN A:220 , GLY A:222 , HOH A:774
BINDING SITE FOR RESIDUE DTD A 505
04
AC4
SOFTWARE
LYS A:335
BINDING SITE FOR RESIDUE CL A 506
05
AC5
SOFTWARE
ASP A:387 , ARG A:389 , HOH A:551 , HOH A:709 , ASP B:453 , THR B:456 , HOH B:562 , HOH B:596
BINDING SITE FOR RESIDUE GOL A 507
06
AC6
SOFTWARE
VAL A:273 , ASN A:274 , LYS A:275 , GLN A:309 , TYR A:310 , HOH A:721
BINDING SITE FOR RESIDUE GOL A 508
07
AC7
SOFTWARE
ARG A:457
BINDING SITE FOR RESIDUE GOL A 509
08
AC8
SOFTWARE
GLN A:241 , ASN A:482 , ILE A:483 , TYR A:485 , HOH A:646 , HOH A:780 , PRO B:299
BINDING SITE FOR RESIDUE GOL A 510
09
AC9
SOFTWARE
ASN A:270 , ASP A:291 , HIS A:459 , ALA A:462 , TYR A:464 , HOH A:539 , HOH A:577
BINDING SITE FOR RESIDUE ACT A 511
10
BC1
SOFTWARE
LYS A:52 , ARG A:68 , ASP A:69 , ASP A:70
BINDING SITE FOR RESIDUE ACT A 512
11
BC2
SOFTWARE
ASN A:261 , GLU A:262 , LEU A:263 , GOL A:524
BINDING SITE FOR RESIDUE ACT A 513
12
BC3
SOFTWARE
ASN A:235 , LYS A:428 , PRO A:429 , HOH A:566 , HOH A:649
BINDING SITE FOR RESIDUE ACT A 514
13
BC4
SOFTWARE
ASN A:482 , GLN A:496
BINDING SITE FOR RESIDUE ACT A 515
14
BC5
SOFTWARE
GLN A:385 , PHE A:394 , HIS A:395 , ARG A:396 , HOH A:692
BINDING SITE FOR RESIDUE ACT A 516
15
BC6
SOFTWARE
ARG A:384 , HOH A:622 , LEU B:430 , ARG B:457
BINDING SITE FOR RESIDUE SO4 A 517
16
BC7
SOFTWARE
LEU A:167 , GLN A:168 , HOH A:919 , THR B:211 , ASP B:213
BINDING SITE FOR RESIDUE GOL A 518
17
BC8
SOFTWARE
LYS A:148 , ASN A:149 , LYS A:157
BINDING SITE FOR RESIDUE GOL A 519
18
BC9
SOFTWARE
SER A:243 , ILE A:246 , TYR A:485 , ALA A:486 , ALA A:489 , HOH A:638 , HOH A:786
BINDING SITE FOR RESIDUE GOL A 520
19
CC1
SOFTWARE
LEU A:92 , VAL A:108 , ASN A:281 , HOH A:934
BINDING SITE FOR RESIDUE GOL A 521
20
CC2
SOFTWARE
PHE A:79 , ASP A:80 , LYS A:115
BINDING SITE FOR RESIDUE GOL A 522
21
CC3
SOFTWARE
GLU A:86 , ARG A:89 , PRO A:144 , PHE A:147 , HIS A:150 , HOH A:549
BINDING SITE FOR RESIDUE GOL A 523
22
CC4
SOFTWARE
THR A:255 , ASN A:261 , ARG A:266 , GLY A:424 , LEU A:425 , ALA A:426 , ACT A:513 , HOH A:677
BINDING SITE FOR RESIDUE GOL A 524
23
CC5
SOFTWARE
GLN A:26
BINDING SITE FOR RESIDUE CL A 525
24
CC6
SOFTWARE
SER A:233 , ASN B:302 , HOH B:673
BINDING SITE FOR RESIDUE CL A 526
25
CC7
SOFTWARE
BHN B:504
BINDING SITE FOR RESIDUE FE B 503
26
CC8
SOFTWARE
TYR B:22 , THR B:23 , MET B:27 , TRP B:100 , ARG B:137 , TRP B:398 , THR B:490 , FE B:503 , HOH B:538 , HOH B:659 , HOH B:924
BINDING SITE FOR RESIDUE BHN B 504
27
CC9
SOFTWARE
TRP B:10 , PRO B:11 , ARG B:205 , GLY B:219 , ASN B:220 , HOH B:527
BINDING SITE FOR RESIDUE DTD B 505
28
DC1
SOFTWARE
GLU B:267 , ASN B:270 , TYR B:271 , SER B:308 , HIS B:459 , ASP B:460 , ALA B:462 , HOH B:594
BINDING SITE FOR RESIDUE GOL B 506
29
DC2
SOFTWARE
ASN A:302 , GLY A:304 , PHE B:229 , ALA B:230 , SER B:233 , THR B:286
BINDING SITE FOR RESIDUE ACT B 507
30
DC3
SOFTWARE
THR B:203 , PRO B:225 , ASP B:227
BINDING SITE FOR RESIDUE ACT B 508
31
DC4
SOFTWARE
ILE B:246 , TYR B:485 , ALA B:486 , HOH B:640 , HOH B:682
BINDING SITE FOR RESIDUE GOL B 509
32
DC5
SOFTWARE
TRP B:10 , MET B:27 , PHE B:28 , HOH B:642
BINDING SITE FOR RESIDUE CL B 510
[
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, 2)
Info
All PROSITE Patterns/Profiles
1: SBP_BACTERIAL_5 (A:51-73,B:51-73)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
SBP_BACTERIAL_5
PS01040
Bacterial extracellular solute-binding proteins, family 5 signature.
NIKA_ECOLI
73-95
2
A:51-73
B:51-73
[
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, 2)
Info
All SCOP Domains
1a: SCOP_d3mz9a_ (A:)
1b: SCOP_d3mz9b_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Periplasmic binding protein-like II
(813)
Superfamily
:
Periplasmic binding protein-like II
(813)
Family
:
Phosphate binding protein-like
(463)
Protein domain
:
Nickel-binding periplasmic protein NikA
(18)
Escherichia coli [TaxId: 562]
(18)
1a
d3mz9a_
A:
1b
d3mz9b_
B:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_SBP_bac_5_3mz9B01 (B:45-419)
1b: PFAM_SBP_bac_5_3mz9B02 (B:45-419)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
PBP
(391)
Family
:
SBP_bac_5
(33)
Escherichia coli (strain K12)
(12)
1a
SBP_bac_5-3mz9B01
B:45-419
1b
SBP_bac_5-3mz9B02
B:45-419
[
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
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 (186 KB)
Header - Asym.Unit
Biol.Unit 1 (94 KB)
Header - Biol.Unit 1
Biol.Unit 2 (90 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
3MZ9
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help