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.
4AFX
Asym. Unit
Info
Asym.Unit (135 KB)
Biol.Unit 1 (130 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 THE REACTIVE LOOP CLEAVED ZPI IN I2 SPACE GROUP
Authors
:
A. Zhou, Y. Yan, Z. Wei
Date
:
23 Jan 12 (Deposition) - 09 Jan 13 (Release) - 09 Jan 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.09
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Hydrolase Inhibitor, Serpin, Protein Z Dependent Inhibitor, Coagulation
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
X. Huang, Y. Yan, Y. Tu, J. Gatti, G. J. J. Broze, A. Zhou, S. T. Olson
Structural Basis For Catalytic Activation Of Protein Z- Dependent Protease Inhibitor (Zpi) By Protein Z.
Blood V. 120 1726 2012
[
close entry info
]
Hetero Components
(3, 6)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
2a: SODIUM ION (NAa)
2b: SODIUM ION (NAb)
3a: PHOSPHATE ION (PO4a)
3b: PHOSPHATE ION (PO4b)
3c: PHOSPHATE ION (PO4c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
1
Ligand/Ion
CALCIUM ION
2
NA
2
Ligand/Ion
SODIUM ION
3
PO4
3
Ligand/Ion
PHOSPHATE ION
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLU A:292
BINDING SITE FOR RESIDUE NA A1387
2
AC2
SOFTWARE
ASN A:159 , ARG A:163
BINDING SITE FOR RESIDUE CA A1388
3
AC3
SOFTWARE
SER A:64 , ARG A:67
BINDING SITE FOR RESIDUE PO4 A1389
4
AC4
SOFTWARE
GLU A:100 , LYS A:104 , PRO A:117 , GLY A:118 , LEU A:120 , PRO A:121
BINDING SITE FOR RESIDUE PO4 A1390
5
AC5
SOFTWARE
GLN A:102
BINDING SITE FOR RESIDUE NA A1391
6
AC6
SOFTWARE
HIS A:73 , GLY A:75 , ASN A:76 , GLN A:323
BINDING SITE FOR RESIDUE PO4 A1392
[
close Site info
]
SAPs(SNPs)/Variants
(9, 9)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_020326 (S40G, chain A, )
2: VAR_038833 (G118R, chain A, )
3: VAR_051940 (L137Q, chain A, )
4: VAR_020327 (T140S, chain A, )
5: VAR_051941 (R175H, chain A, )
6: VAR_038834 (G250S, chain A, )
7: VAR_038835 (Q363P, chain A, )
8: VAR_051942 (Q363R, chain A, )
9: VAR_070192 (F399L, chain B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_020326
S
61
G
ZPI_HUMAN
Polymorphism
941591
A
S
40
G
2
UniProt
VAR_038833
G
139
R
ZPI_HUMAN
Polymorphism
56137907
A
G
118
R
3
UniProt
VAR_051940
L
158
Q
ZPI_HUMAN
Polymorphism
2232699
A
L
137
Q
4
UniProt
VAR_020327
T
161
S
ZPI_HUMAN
Polymorphism
2232700
A
T
140
S
5
UniProt
VAR_051941
R
196
H
ZPI_HUMAN
Polymorphism
2232701
A
R
175
H
6
UniProt
VAR_038834
G
271
S
ZPI_HUMAN
Polymorphism
2232708
A
G
250
S
7
UniProt
VAR_038835
Q
384
P
ZPI_HUMAN
Polymorphism
---
A
Q
363
P
8
UniProt
VAR_051942
Q
384
R
ZPI_HUMAN
Polymorphism
2232710
A
Q
363
R
9
UniProt
VAR_070192
F
420
L
ZPI_HUMAN
Polymorphism
---
B
F
399
L
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
(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
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
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
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 (135 KB)
Header - Asym.Unit
Biol.Unit 1 (130 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
4AFX
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
