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.
1ZLQ
Asym. Unit
Info
Asym.Unit (367 KB)
Biol.Unit 1 (185 KB)
Biol.Unit 2 (181 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTALLOGRAPHIC AND SPECTROSCOPIC EVIDENCE FOR HIGH AFFINITY BINDING OF FE EDTA (H2O)- TO THE PERIPLASMIC NICKEL TRANSPORTER NIKA
Authors
:
M. V. Cherrier, L. Martin, C. Cavazza, L. Jacquamet, D. Lemaire, J. Gail J. C. Fontecilla Camps
Date
:
09 May 05 (Deposition) - 02 Aug 05 (Release) - 13 Jul 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
:
Nickel, Edta, Transport, Bacteria, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. V. Cherrier, L. Martin, C. Cavazza, L. Jacquamet, D. Lemaire, J. Gaillard, J. C. Fontecilla Camps
Crystallographic And Spectroscopic Evidence For High Affinity Binding Of Feedta(H(2)O)(-) To The Periplasmic Nickel Transporter Nika
J. Am. Chem. Soc. V. 127 10075 2005
[
close entry info
]
Hetero Components
(7, 25)
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)
1i: ACETATE ION (ACTi)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
2e: CHLORIDE ION (CLe)
3a: 2,3-DIHYDROXY-1,4-DITHIOBUTANE (DTTa)
4a: {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL... (EDTa)
4b: {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL... (EDTb)
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)
7a: SULFATE ION (SO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
9
Ligand/Ion
ACETATE ION
2
CL
5
Ligand/Ion
CHLORIDE ION
3
DTT
1
Ligand/Ion
2,3-DIHYDROXY-1,4-DITHIOBUTANE
4
EDT
2
Ligand/Ion
{[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID
5
FE
2
Ligand/Ion
FE (III) ION
6
GOL
5
Ligand/Ion
GLYCEROL
7
SO4
1
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(25, 25)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
EDT A:1513
BINDING SITE FOR RESIDUE FE A 1501
02
AC2
SOFTWARE
EDT B:1511 , HOH B:1514
BINDING SITE FOR RESIDUE FE B 1502
03
AC3
SOFTWARE
PRO A:11 , GLY A:219 , ASN A:220 , GLY A:222 , LEU A:223 , HOH A:1927
BINDING SITE FOR RESIDUE ACT A 1502
04
AC4
SOFTWARE
TYR B:382 , GLN B:385 , PHE B:394 , HIS B:395 , ARG B:396 , HOH B:1609
BINDING SITE FOR RESIDUE ACT B 1503
05
AC5
SOFTWARE
LYS A:52 , ARG A:68 , ASP A:69 , ASP A:70 , HOH A:1883
BINDING SITE FOR RESIDUE ACT A 1503
06
AC6
SOFTWARE
THR B:23 , GLN B:26
BINDING SITE FOR RESIDUE ACT B 1504
07
AC7
SOFTWARE
ASN A:261 , GLU A:262 , LEU A:263 , HOH A:1576 , HOH A:1589 , HOH A:1877
BINDING SITE FOR RESIDUE ACT A 1504
08
AC8
SOFTWARE
ASN A:235 , ALA A:237 , PHE A:419 , GLN A:423 , HOH A:1600 , HOH A:1709
BINDING SITE FOR RESIDUE ACT A 1505
09
AC9
SOFTWARE
ASN A:482 , GLN A:496 , HOH A:1801 , ASP B:43
BINDING SITE FOR RESIDUE ACT A 1506
10
BC1
SOFTWARE
GLN A:385 , PHE A:394 , HIS A:395 , ARG A:396 , HOH A:1648
BINDING SITE FOR RESIDUE ACT A 1507
11
BC2
SOFTWARE
VAL B:273 , LYS B:275 , LYS B:276 , TYR B:310
BINDING SITE FOR RESIDUE ACT B 1505
12
BC3
SOFTWARE
ARG A:384 , HOH A:1805 , HOH A:1897 , HOH A:1908 , LEU B:430 , ARG B:457
BINDING SITE FOR RESIDUE SO4 A 1508
13
BC4
SOFTWARE
GLN A:26
BINDING SITE FOR RESIDUE CL A 1509
14
BC5
SOFTWARE
ASP A:331 , ARG A:365
BINDING SITE FOR RESIDUE CL A 1510
15
BC6
SOFTWARE
ARG A:97 , HOH A:1642 , LYS B:306 , LYS B:314
BINDING SITE FOR RESIDUE CL A 1511
16
BC7
SOFTWARE
MET B:27 , PHE B:28 , THR B:490
BINDING SITE FOR RESIDUE CL B 1506
17
BC8
SOFTWARE
PHE A:229 , SER A:233 , ASN B:302
BINDING SITE FOR RESIDUE CL A 1512
18
BC9
SOFTWARE
TYR A:22 , MET A:27 , ARG A:97 , TRP A:100 , ARG A:137 , TRP A:398 , HIS A:416 , THR A:490 , FE A:1501 , HOH A:1647 , HOH A:1747 , HOH A:1903 , HOH A:1937
BINDING SITE FOR RESIDUE EDT A 1513
19
CC1
SOFTWARE
TYR B:22 , ARG B:97 , TRP B:100 , ARG B:137 , TRP B:398 , THR B:490 , FE B:1502 , HOH B:1514 , HOH B:1520 , HOH B:1603 , HOH B:1613 , HOH B:1868
BINDING SITE FOR RESIDUE EDT B 1511
20
CC2
SOFTWARE
ARG A:89 , LEU A:92 , ARG A:95 , VAL A:108 , ASP A:109 , VAL A:110 , ASN A:281 , GLU A:358 , ILE A:359 , ALA A:362 , HOH A:1972 , HOH A:1976 , HOH A:1987
BINDING SITE FOR RESIDUE DTT A 1514
21
CC3
SOFTWARE
LEU A:167 , GLN A:168 , HOH A:1683 , THR B:211 , ASP B:213
BINDING SITE FOR RESIDUE GOL A 1515
22
CC4
SOFTWARE
TRP B:10 , PRO B:11 , GLY B:219 , ASN B:220 , GLY B:222 , LEU B:223 , HOH B:1847 , HOH B:1862
BINDING SITE FOR RESIDUE GOL B 1512
23
CC5
SOFTWARE
LYS A:148 , ASN A:149 , LYS A:157 , HOH A:1887 , HOH A:1931
BINDING SITE FOR RESIDUE GOL A 1516
24
CC6
SOFTWARE
LYS A:111 , GLU A:358 , GLN A:361 , SER A:372 , LEU A:373
BINDING SITE FOR RESIDUE GOL A 1517
25
CC7
SOFTWARE
SER B:57 , ASP B:59 , LYS B:61 , HOH B:1884
BINDING SITE FOR RESIDUE GOL B 1513
[
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_d1zlqa1 (A:3-501)
1b: SCOP_d1zlqb_ (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
d1zlqa1
A:3-501
1b
d1zlqb_
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_1zlqB01 (B:45-419)
1b: PFAM_SBP_bac_5_1zlqB02 (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_5-1zlqB01
B:45-419
1b
SBP_bac_5-1zlqB02
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 (367 KB)
Header - Asym.Unit
Biol.Unit 1 (185 KB)
Header - Biol.Unit 1
Biol.Unit 2 (181 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
1ZLQ
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help