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.
4DDJ
Asym. Unit
Info
Asym.Unit (48 KB)
Biol.Unit 1 (80 KB)
Biol.Unit 2 (41 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 SAPOSIN A IN COMPLEX WITH LAURYLDIMETHYLAMINE-N-OXIDE (LDAO)
Authors
:
K. Popovic, G. G. Prive
Date
:
18 Jan 12 (Deposition) - 15 Feb 12 (Release) - 14 Mar 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A
Biol. Unit 1: A (2x)
Biol. Unit 2: A (1x)
Keywords
:
Saposin Fold, Sphingolipid Activator Protein, Galactosylceramide, Lauryldimethylamine-N-Oxide, Lipid, Detergent, Lysosome, Lipid Binding Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Popovic, J. Holyoake, R. Pomes, G. G. Prive
Structure Of Saposin A Lipoprotein Discs.
Proc. Natl. Acad. Sci. Usa V. 109 2908 2012
[
close entry info
]
Hetero Components
(1, 20)
Info
All Hetero Components
1a: LAURYL DIMETHYLAMINE-N-OXIDE (LDAa)
1b: LAURYL DIMETHYLAMINE-N-OXIDE (LDAb)
1c: LAURYL DIMETHYLAMINE-N-OXIDE (LDAc)
1d: LAURYL DIMETHYLAMINE-N-OXIDE (LDAd)
1e: LAURYL DIMETHYLAMINE-N-OXIDE (LDAe)
1f: LAURYL DIMETHYLAMINE-N-OXIDE (LDAf)
1g: LAURYL DIMETHYLAMINE-N-OXIDE (LDAg)
1h: LAURYL DIMETHYLAMINE-N-OXIDE (LDAh)
1i: LAURYL DIMETHYLAMINE-N-OXIDE (LDAi)
1j: LAURYL DIMETHYLAMINE-N-OXIDE (LDAj)
1k: LAURYL DIMETHYLAMINE-N-OXIDE (LDAk)
1l: LAURYL DIMETHYLAMINE-N-OXIDE (LDAl)
1m: LAURYL DIMETHYLAMINE-N-OXIDE (LDAm)
1n: LAURYL DIMETHYLAMINE-N-OXIDE (LDAn)
1o: LAURYL DIMETHYLAMINE-N-OXIDE (LDAo)
1p: LAURYL DIMETHYLAMINE-N-OXIDE (LDAp)
1q: LAURYL DIMETHYLAMINE-N-OXIDE (LDAq)
1r: LAURYL DIMETHYLAMINE-N-OXIDE (LDAr)
1s: LAURYL DIMETHYLAMINE-N-OXIDE (LDAs)
1t: LAURYL DIMETHYLAMINE-N-OXIDE (LDAt)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
LDA
20
Ligand/Ion
LAURYL DIMETHYLAMINE-N-OXIDE
[
close Hetero Component info
]
Sites
(20, 20)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TYR A:30 , THR A:34 , TRP A:37
BINDING SITE FOR RESIDUE LDA A 101
02
AC2
SOFTWARE
ASP A:20 , THR A:23 , GLU A:26 , LDA A:103 , LDA A:109
BINDING SITE FOR RESIDUE LDA A 102
03
AC3
SOFTWARE
GLU A:26 , TYR A:30 , LDA A:102 , LDA A:109
BINDING SITE FOR RESIDUE LDA A 103
04
AC4
SOFTWARE
LEU A:76 , ASN A:77 , LDA A:106 , LDA A:114 , LDA A:117
BINDING SITE FOR RESIDUE LDA A 104
05
AC5
SOFTWARE
TYR A:54 , ALA A:75 , ASN A:77 , LDA A:110 , LDA A:117 , LDA A:118
BINDING SITE FOR RESIDUE LDA A 105
06
AC6
SOFTWARE
VAL A:10 , LDA A:104 , LDA A:115 , HOH A:232
BINDING SITE FOR RESIDUE LDA A 106
07
AC7
SOFTWARE
TYR A:30 , LDA A:108 , LDA A:109 , HOH A:252
BINDING SITE FOR RESIDUE LDA A 107
08
AC8
SOFTWARE
LDA A:107 , LDA A:114 , LDA A:119
BINDING SITE FOR RESIDUE LDA A 108
09
AC9
SOFTWARE
LDA A:102 , LDA A:103 , LDA A:107 , LDA A:119
BINDING SITE FOR RESIDUE LDA A 109
10
BC1
SOFTWARE
ALA A:75 , LDA A:105
BINDING SITE FOR RESIDUE LDA A 110
11
BC2
SOFTWARE
GLU A:65 , GLU A:71 , LDA A:112 , LDA A:113 , LDA A:116 , HOH A:253
BINDING SITE FOR RESIDUE LDA A 111
12
BC3
SOFTWARE
LDA A:111 , LDA A:116 , LDA A:119
BINDING SITE FOR RESIDUE LDA A 112
13
BC4
SOFTWARE
VAL A:10 , MET A:66 , LDA A:111 , LDA A:115 , LDA A:119
BINDING SITE FOR RESIDUE LDA A 113
14
BC5
SOFTWARE
TRP A:37 , LDA A:104 , LDA A:108 , LDA A:117
BINDING SITE FOR RESIDUE LDA A 114
15
BC6
SOFTWARE
LEU A:38 , MET A:43 , LDA A:106 , LDA A:113 , LDA A:117 , LDA A:120
BINDING SITE FOR RESIDUE LDA A 115
16
BC7
SOFTWARE
LDA A:111 , LDA A:112
BINDING SITE FOR RESIDUE LDA A 116
17
BC8
SOFTWARE
THR A:34 , TRP A:37 , CYS A:47 , VAL A:51 , LDA A:104 , LDA A:105 , LDA A:114 , LDA A:115
BINDING SITE FOR RESIDUE LDA A 117
18
BC9
SOFTWARE
GLU A:25 , LEU A:28 , GLU A:32 , TYR A:54 , ILE A:61 , LDA A:105
BINDING SITE FOR RESIDUE LDA A 118
19
CC1
SOFTWARE
MET A:17 , LEU A:18 , LDA A:108 , LDA A:109 , LDA A:112 , LDA A:113
BINDING SITE FOR RESIDUE LDA A 119
20
CC2
SOFTWARE
ASP A:9 , LDA A:115
BINDING SITE FOR RESIDUE LDA A 120
[
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
(3, 3)
Info
All Exons
Exon 1.3 (A:1-24)
Exon 1.4b (A:25-66)
Exon 1.5 (A:67-80)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.2/1.3
2: Boundary 1.3/1.4b
3: Boundary 1.4b/1.5
4: Boundary 1.5/1.6
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
1.1a
ENST00000394936
1a
ENSE00001858117
chr10:
73611126-73610939
188
SAP_HUMAN
1-14
14
0
-
-
1.2
ENST00000394936
2
ENSE00001239781
chr10:
73594262-73594129
134
SAP_HUMAN
14-58
45
0
-
-
1.3
ENST00000394936
3
ENSE00000987087
chr10:
73591677-73591603
75
SAP_HUMAN
59-83
25
1
A:1-24
24
1.4b
ENST00000394936
4b
ENSE00000987088
chr10:
73591008-73590883
126
SAP_HUMAN
84-125
42
1
A:25-66
42
1.5
ENST00000394936
5
ENSE00001239733
chr10:
73588834-73588634
201
SAP_HUMAN
126-192
67
1
A:67-80
14
1.6
ENST00000394936
6
ENSE00000987090
chr10:
73587914-73587771
144
SAP_HUMAN
193-240
48
0
-
-
1.7
ENST00000394936
7
ENSE00000987091
chr10:
73585650-73585594
57
SAP_HUMAN
241-259
19
0
-
-
1.10c
ENST00000394936
10c
ENSE00001239711
chr10:
73581764-73581633
132
SAP_HUMAN
260-303
44
0
-
-
1.11
ENST00000394936
11
ENSE00000987093
chr10:
73580092-73579997
96
SAP_HUMAN
304-335
32
0
-
-
1.12b
ENST00000394936
12b
ENSE00000987094
chr10:
73579657-73579471
187
SAP_HUMAN
336-398
63
0
-
-
1.13
ENST00000394936
13
ENSE00000987095
chr10:
73579379-73579222
158
SAP_HUMAN
398-450
53
0
-
-
1.14b
ENST00000394936
14b
ENSE00000987096
chr10:
73578868-73578788
81
SAP_HUMAN
451-477
27
0
-
-
1.15b
ENST00000394936
15b
ENSE00000987097
chr10:
73578481-73578374
108
SAP_HUMAN
478-513
36
0
-
-
1.16e
ENST00000394936
16e
ENSE00001917960
chr10:
73577233-73576055
1179
SAP_HUMAN
514-524
11
0
-
-
[
close EXON info
]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d4ddja_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Saposin-like
(21)
Superfamily
:
Saposin
(17)
Family
:
NKL-like
(13)
Protein domain
:
Saposin C
(11)
Human (Homo sapiens) [TaxId: 9606]
(11)
1a
d4ddja_
A:
[
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
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 (48 KB)
Header - Asym.Unit
Biol.Unit 1 (80 KB)
Header - Biol.Unit 1
Biol.Unit 2 (41 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
4DDJ
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help