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.
3CMP
Asym. Unit
Info
Asym.Unit (92 KB)
Biol.Unit 1 (32 KB)
Biol.Unit 2 (27 KB)
Biol.Unit 3 (33 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF SIDEROCALIN (NGAL, LIPOCALIN 2) K125A MUTANT COMPLEXED WITH FERRIC ENTEROBACTIN
Authors
:
M. C. Clifton, R. K. Strong
Date
:
24 Mar 08 (Deposition) - 12 May 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Keywords
:
Lipocalin, Siderocalin, Enterobactin, Siderophore, Iron, Glycoprotein, Pyrrolidone Carboxylic Acid, Secreted, Antimicrobial Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. C. Clifton, J. C. Pizzaro, R. Abergel, T. Hoette, V. Vigdorovich, K. Raymond, R. K. Strong
Structural Studies Of Human Siderocalin
To Be Published
[
close entry info
]
Hetero Components
(6, 20)
Info
All Hetero Components
1a: 2,3-DIHYDROXY-BENZOIC ACID (DBHa)
1b: 2,3-DIHYDROXY-BENZOIC ACID (DBHb)
2a: N,N',N''-[(3S,7S,11S)-2,6,10-TRIOX... (EB4a)
2b: N,N',N''-[(3S,7S,11S)-2,6,10-TRIOX... (EB4b)
3a: FE (III) ION (FEa)
3b: FE (III) ION (FEb)
3c: FE (III) ION (FEc)
4a: GLYCEROL (GOLa)
4b: GLYCEROL (GOLb)
4c: GLYCEROL (GOLc)
5a: SODIUM ION (NAa)
5b: SODIUM ION (NAb)
5c: SODIUM ION (NAc)
5d: SODIUM ION (NAd)
5e: SODIUM ION (NAe)
5f: SODIUM ION (NAf)
5g: SODIUM ION (NAg)
6a: SULFATE ION (SO4a)
6b: SULFATE ION (SO4b)
6c: SULFATE ION (SO4c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DBH
2
Ligand/Ion
2,3-DIHYDROXY-BENZOIC ACID
2
EB4
2
Ligand/Ion
N,N',N''-[(3S,7S,11S)-2,6,10-TRIOXO-1,5,9-TRIOXACYCLODODECANE-3,7,11-TRIYL]TRIS(2,3-DIHYDROXYBENZAMIDE)
3
FE
3
Ligand/Ion
FE (III) ION
4
GOL
3
Ligand/Ion
GLYCEROL
5
NA
7
Ligand/Ion
SODIUM ION
6
SO4
3
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(17, 17)
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: AD1 (SOFTWARE)
11: AD2 (SOFTWARE)
12: BC1 (SOFTWARE)
13: BC3 (SOFTWARE)
14: BC4 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
EB4 A:183
BINDING SITE FOR RESIDUE FE A 179
02
AC2
SOFTWARE
TYR A:52 , LYS A:134 , EB4 A:183
BINDING SITE FOR RESIDUE NA A 180
03
AC3
SOFTWARE
VAL A:33 , TYR A:52 , THR A:54 , SER A:68 , ARG A:81 , PHE A:123 , LYS A:134 , THR A:136 , TYR A:138 , EB4 A:183
BINDING SITE FOR RESIDUE SO4 A 181
04
AC4
SOFTWARE
ASN A:164 , HIS A:165 , HOH A:189 , HOH A:201 , LYS C:75
BINDING SITE FOR RESIDUE SO4 A 182
05
AC5
SOFTWARE
LYS B:134 , DBH B:303 , DBH B:304
BINDING SITE FOR RESIDUE FE B 179
06
AC6
SOFTWARE
THR B:54
BINDING SITE FOR RESIDUE NA B 180
07
AC7
SOFTWARE
EB4 C:186
BINDING SITE FOR RESIDUE FE C 179
08
AC8
SOFTWARE
THR C:54 , TYR C:138
BINDING SITE FOR RESIDUE NA C 180
09
AC9
SOFTWARE
TYR C:52 , LYS C:134
BINDING SITE FOR RESIDUE NA C 181
10
AD1
SOFTWARE
ALA A:40 , TRP A:79 , LEU A:103 , TYR A:106 , PHE A:123 , SER A:127 , TYR A:132 , LYS A:134 , FE A:179 , NA A:180 , SO4 A:181 , HOH A:185 , HOH A:193
BINDING SITE FOR RESIDUE EB4 A 183
11
AD2
SOFTWARE
ALA C:40 , ARG C:72 , TRP C:79 , LEU C:103 , TYR C:106 , PHE C:123 , SER C:127 , TYR C:132 , LYS C:134 , FE C:179 , GOL C:188 , HOH C:189
BINDING SITE FOR RESIDUE EB4 C 186
12
BC1
SOFTWARE
LYS A:75 , ASN C:164 , HIS C:165
BINDING SITE FOR RESIDUE SO4 C 185
13
BC3
SOFTWARE
ALA B:40 , TYR B:106 , PHE B:123 , LYS B:134 , FE B:179 , DBH B:304
BINDING SITE FOR RESIDUE DBH B 303
14
BC4
SOFTWARE
FE B:179 , DBH B:303
BINDING SITE FOR RESIDUE DBH B 304
15
BC6
SOFTWARE
ASN A:114 , HIS A:118 , ASN B:116 , ASN C:116
BINDING SITE FOR RESIDUE GOL A 184
16
BC7
SOFTWARE
GLY C:86 , SER C:87 , ILE C:97 , SER C:105 , TYR C:106
BINDING SITE FOR RESIDUE GOL C 187
17
BC8
SOFTWARE
EB4 C:186 , HOH C:231
BINDING SITE FOR RESIDUE GOL C 188
[
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, 3)
Info
All PROSITE Patterns/Profiles
1: LIPOCALIN (A:21-34,B:21-34,C:21-34)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
LIPOCALIN
PS00213
Lipocalin signature.
NGAL_HUMAN
41-54
3
A:21-34
B:21-34
C:21-34
[
close PROSITE info
]
Exons
(6, 18)
Info
All Exons
Exon 1.2d (A:5-26 | B:5-26 | C:4-26)
Exon 1.3 (A:27-72 | B:27-72 (gaps) | C:27-72)
Exon 1.6b (A:72-99 | B:72-99 | C:72-99)
Exon 1.7 (A:99-139 | B:99-139 | C:99-139)
Exon 1.8 (A:139-173 | B:139-173 (gaps) | C:1...)
Exon 1.9b (A:173-178 | B:173-178 | C:173-177)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.1/1.2d
2: Boundary 1.2d/1.3
3: Boundary 1.3/1.6b
4: Boundary 1.6b/1.7
5: Boundary 1.7/1.8
6: Boundary 1.8/1.9b
7: Boundary 1.9b/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1
ENST00000373017
1
ENSE00001459333
chr9:
130911350-130911543
194
NGAL_HUMAN
-
0
0
-
-
1.2d
ENST00000373017
2d
ENSE00001459332
chr9:
130911762-130911942
181
NGAL_HUMAN
1-46
46
3
A:5-26
B:5-26
C:4-26
22
22
23
1.3
ENST00000373017
3
ENSE00000984625
chr9:
130912517-130912653
137
NGAL_HUMAN
47-92
46
3
A:27-72
B:27-72 (gaps)
C:27-72
46
46
46
1.6b
ENST00000373017
6b
ENSE00000984626
chr9:
130913917-130913996
80
NGAL_HUMAN
92-119
28
3
A:72-99
B:72-99
C:72-99
28
28
28
1.7
ENST00000373017
7
ENSE00000984627
chr9:
130914185-130914304
120
NGAL_HUMAN
119-159
41
3
A:99-139
B:99-139
C:99-139
41
41
41
1.8
ENST00000373017
8
ENSE00001419823
chr9:
130914462-130914563
102
NGAL_HUMAN
159-193
35
3
A:139-173
B:139-173 (gaps)
C:139-173
35
35
35
1.9b
ENST00000373017
9b
ENSE00001459311
chr9:
130915379-130915412
34
NGAL_HUMAN
193-198
6
3
A:173-178
B:173-178
C:173-177
6
6
5
[
close EXON info
]
SCOP Domains
(1, 3)
Info
All SCOP Domains
1a: SCOP_d3cmpa_ (A:)
1b: SCOP_d3cmpb_ (B:)
1c: SCOP_d3cmpc_ (C:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Lipocalins
(514)
Superfamily
:
Lipocalins
(514)
Family
:
Retinol binding protein-like
(261)
Protein domain
:
Neutrophil gelatinase-associated lipocalin (NGAL)
(28)
Human (Homo sapiens) [TaxId: 9606]
(28)
1a
d3cmpa_
A:
1b
d3cmpb_
B:
1c
d3cmpc_
C:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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 (92 KB)
Header - Asym.Unit
Biol.Unit 1 (32 KB)
Header - Biol.Unit 1
Biol.Unit 2 (27 KB)
Header - Biol.Unit 2
Biol.Unit 3 (33 KB)
Header - Biol.Unit 3
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
3CMP
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
