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.
PLEASE WAIT...
Getting 'Exon' information from database.
1L8L
Asym. Unit
Info
Asym.Unit (78 KB)
Biol.Unit 1 (71 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
MOLECULAR BASIS FOR THE LOCAL CONFOMATIONAL REARRANGEMENT OF HUMAN PHOSPHOSERINE PHOSPHATASE
Authors
:
H. Y. Kim, Y. S. Heo, J. H. Kim, M. H. Park, J. Moon, S. Y. Park, T. G. Lee, Y. H. Jeon, S. Ro, K. Y. Hwang
Date
:
21 Mar 02 (Deposition) - 01 Apr 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.51
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Phosphatase, Conformational Rearrangement, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Y. Kim, Y. S. Heo, J. H. Kim, M. H. Park, J. Moon, E. Kim, D. Kwon, J. Yoon, D. Shin, E. J. Jeong, S. Y. Park, T. G. Lee, Y. H. Jeon, S. Ro, J. M. Cho, K. Y. Hwang
Molecular Basis For The Local Conformational Rearrangement Of Human Phosphoserine Phosphatase.
J. Biol. Chem. V. 277 46651 2002
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 2)
Info
All Hetero Components
1a: D-2-AMINO-3-PHOSPHONO-PROPIONIC AC... (APOa)
1b: D-2-AMINO-3-PHOSPHONO-PROPIONIC AC... (APOb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
APO
2
Ligand/Ion
D-2-AMINO-3-PHOSPHONO-PROPIONIC ACID
[
close Hetero Component info
]
Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:20 , ASP A:22 , GLU A:29 , SER A:109 , GLY A:110 , LYS A:158 , ASP A:179 , GLY A:180 , THR A:182
BINDING SITE FOR RESIDUE APO A 800
2
AC2
SOFTWARE
ASP B:20 , VAL B:21 , ASP B:22 , SER B:109 , GLY B:110 , LYS B:158 , THR B:182 , ASP B:183 , ARG B:202
BINDING SITE FOR RESIDUE APO B 801
[
close Site info
]
SAPs(SNPs)/Variants
(2, 4)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_022378 (D32N, chain A/B, )
2: VAR_022379 (M52T, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_022378
D
32
N
SERB_HUMAN
Disease (PSPHD)
28933976
A/B
D
32
N
2
UniProt
VAR_022379
M
52
T
SERB_HUMAN
Disease (PSPHD)
---
A/B
M
52
T
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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
(5, 10)
Info
All Exons
Exon 1.6c (A:4-47 | B:4-47)
Exon 1.7b (A:47-92 | B:47-92)
Exon 1.8b (A:92-141 | B:92-141)
Exon 1.9b (A:141-190 | B:141-190)
Exon 1.10c (A:191-225 | B:191-225)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.5a/1.6c
2: Boundary 1.6c/1.7b
3: Boundary 1.7b/1.8b
4: Boundary 1.8b/1.9b
5: Boundary 1.9b/1.10c
6: Boundary 1.10c/-
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
ENST00000395471
1a
ENSE00001749046
chr7:
56119297-56118831
467
SERB_HUMAN
-
0
0
-
-
1.3d
ENST00000395471
3d
ENSE00001638092
chr7:
56101847-56101654
194
SERB_HUMAN
-
0
0
-
-
1.5a
ENST00000395471
5a
ENSE00001337387
chr7:
56099747-56099622
126
SERB_HUMAN
-
0
0
-
-
1.6c
ENST00000395471
6c
ENSE00002171169
chr7:
56088924-56088766
159
SERB_HUMAN
1-47
47
2
A:4-47
B:4-47
44
44
1.7b
ENST00000395471
7b
ENSE00001018705
chr7:
56087427-56087293
135
SERB_HUMAN
47-92
46
2
A:47-92
B:47-92
46
46
1.8b
ENST00000395471
8b
ENSE00001121162
chr7:
56085072-56084927
146
SERB_HUMAN
92-141
50
2
A:92-141
B:92-141
50
50
1.9b
ENST00000395471
9b
ENSE00000976989
chr7:
56082864-56082716
149
SERB_HUMAN
141-190
50
2
A:141-190
B:141-190
50
50
1.10c
ENST00000395471
10c
ENSE00001521802
chr7:
56079562-56078761
802
SERB_HUMAN
191-225
35
2
A:191-225
B:191-225
35
35
[
close EXON info
]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1l8la_ (A:)
1b: SCOP_d1l8lb_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
HAD-like
(349)
Superfamily
:
HAD-like
(349)
Family
:
Phosphoserine phosphatase
(9)
Protein domain
:
Phosphoserine phosphatase
(9)
Human (Homo sapiens) [TaxId: 9606]
(3)
1a
d1l8la_
A:
1b
d1l8lb_
B:
[
close SCOP info
]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1l8lA01 (A:4-29,A:81-134,A:147-225)
1b: CATH_1l8lB01 (B:4-29,B:81-134,B:147-225)
2a: CATH_1l8lA02 (A:30-80,A:135-146)
2b: CATH_1l8lB02 (B:30-80,B:135-146)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.1000, no name defined]
(211)
Human (Homo sapiens)
(42)
1a
1l8lA01
A:4-29,A:81-134,A:147-225
1b
1l8lB01
B:4-29,B:81-134,B:147-225
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
DNA polymerase; domain 1
(617)
Homologous Superfamily
:
Phosphoserine phosphatase; domain 2
(9)
Human (Homo sapiens)
(3)
2a
1l8lA02
A:30-80,A:135-146
2b
1l8lB02
B:30-80,B:135-146
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_Hydrolase_1l8lB01 (B:14-191)
1b: PFAM_Hydrolase_1l8lB02 (B:14-191)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
HAD
(186)
Family
:
Hydrolase
(64)
Homo sapiens (Human)
(6)
1a
Hydrolase-1l8lB01
B:14-191
1b
Hydrolase-1l8lB02
B:14-191
[
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 (78 KB)
Header - Asym.Unit
Biol.Unit 1 (71 KB)
Header - Biol.Unit 1
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
1L8L
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help