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...
Getting 'PROSITE' information from database.
1J78
Biol. Unit 2
Info
Asym.Unit (152 KB)
Biol.Unit 1 (73 KB)
Biol.Unit 2 (76 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTALLOGRAPHIC ANALYSIS OF THE HUMAN VITAMIN D BINDING PROTEIN
Authors
:
C. Verboven, A. Rabijns, M. De Maeyer, H. Van Baelen, R. Bouillon, C. De Ranter
Date
:
16 May 01 (Deposition) - 06 Feb 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.31
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Plasma Protein, Vitamin D Binding, Actin Binding, Fatty Acid Binding, Gc-Globulin, Group-Specific Component, Transport, Ligand Binding Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. Verboven, A. Rabijns, M. De Maeyer, H. Van Baelen, R. Bouillon, C. De Ranter
A Structural Basis For The Unique Binding Features Of The Human Vitamin D-Binding Protein.
Nat. Struct. Biol. V. 9 131 2002
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 3)
Info
All Hetero Components
1a: OLEIC ACID (OLAa)
1b: OLEIC ACID (OLAb)
1c: OLEIC ACID (OLAc)
2a: 3-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HE... (VDYa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
OLA
2
Ligand/Ion
OLEIC ACID
2
VDY
1
Ligand/Ion
3-{2-[1-(5-HYDROXY-1,5-DIMETHYL-HEXYL)-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE]-ETHYLIDENE}-4-METHYLENE-CYCLOHEXANOL
[
close Hetero Component info
]
Sites
(3, 3)
Info
All Sites
1: AC2 (SOFTWARE)
2: AC3 (SOFTWARE)
3: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC2
SOFTWARE
LYS B:347 , GLU B:379
BINDING SITE FOR RESIDUE OLA B 459
2
AC3
SOFTWARE
LYS A:354 , ASP A:361 , GLU A:363 , GLN B:153 , TYR B:207 , ALA B:208 , TYR B:210 , GLU B:251
BINDING SITE FOR RESIDUE OLA B 460
3
AC4
SOFTWARE
GLU B:8 , VAL B:12 , LEU B:31 , TYR B:32 , LYS B:35 , TYR B:68 , SER B:76 , MET B:107 , HOH B:597
BINDING SITE FOR RESIDUE VDY B 500
[
close Site info
]
SAPs(SNPs)/Variants
(4, 4)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_000548 (D416E, chain B, )
2: VAR_000549 (T420T, chain B, )
3: VAR_014120 (R429C, chain B, )
4: VAR_014121 (R429H, chain B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_000548
D
432
E
VTDB_HUMAN
Polymorphism
7041
B
D
416
E
2
UniProt
VAR_000549
K
436
T
VTDB_HUMAN
Polymorphism
4588
B
T
420
T
3
UniProt
VAR_014120
R
445
C
VTDB_HUMAN
Polymorphism
---
B
R
429
C
4
UniProt
VAR_014121
R
445
H
VTDB_HUMAN
Polymorphism
9016
B
R
429
H
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: ALBUMIN_2 (B:193-378)
2: ALBUMIN_1 (B:166-190)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ALBUMIN_2
PS51438
Albumin domain profile.
VTDB_HUMAN
16-208
209-394
1
-
-
B:193-378
2
ALBUMIN_1
PS00212
Albumin domain signature.
VTDB_HUMAN
182-206
1
-
B:166-190
[
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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 6)
Info
All SCOP Domains
1a: SCOP_d1j78a1 (A:13-198)
1b: SCOP_d1j78a2 (A:199-386)
1c: SCOP_d1j78a3 (A:387-457)
1d: SCOP_d1j78b1 (B:3-198)
1e: SCOP_d1j78b2 (B:199-386)
1f: SCOP_d1j78b3 (B:387-456)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Serum albumin-like
(99)
Superfamily
:
Serum albumin-like
(99)
Family
:
Serum albumin-like
(75)
Protein domain
:
Vitamin D binding protein
(6)
Human (Homo sapiens) [TaxId: 9606]
(6)
1a
d1j78a1
A:13-198
1b
d1j78a2
A:199-386
1c
d1j78a3
A:387-457
1d
d1j78b1
B:3-198
1e
d1j78b2
B:199-386
1f
d1j78b3
B:387-456
[
close SCOP info
]
CATH Domains
(1, 10)
Info
all CATH domains
1a: CATH_1j78A02 (A:124-211)
1b: CATH_1j78B02 (B:124-211)
1c: CATH_1j78A03 (A:212-299)
1d: CATH_1j78B03 (B:212-299)
1e: CATH_1j78A01 (A:13-111)
1f: CATH_1j78B01 (B:7-111)
1g: CATH_1j78A04 (A:315-391)
1h: CATH_1j78B04 (B:315-391)
1i: CATH_1j78A05 (A:398-457)
1j: CATH_1j78B05 (B:398-456)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Serum Albumin; Chain A, Domain 1
(74)
Homologous Superfamily
:
[code=1.10.246.10, no name defined]
(60)
Human (Homo sapiens)
(57)
1a
1j78A02
A:124-211
1b
1j78B02
B:124-211
1c
1j78A03
A:212-299
1d
1j78B03
B:212-299
1e
1j78A01
A:13-111
1f
1j78B01
B:7-111
1g
1j78A04
A:315-391
1h
1j78B04
B:315-391
1i
1j78A05
A:398-457
1j
1j78B05
B:398-456
[
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 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 (152 KB)
Header - Asym.Unit
Biol.Unit 1 (73 KB)
Header - Biol.Unit 1
Biol.Unit 2 (76 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
1J78
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help