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.
1IVY
Asym. Unit
Info
Asym.Unit (159 KB)
Biol.Unit 1 (153 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
PHYSIOLOGICAL DIMER HPP PRECURSOR
Authors
:
G. Rudenko, E. Bonten, A. D'Azzo, W. G. J. Hol
Date
:
12 Jun 96 (Deposition) - 21 Apr 97 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Carboxypeptidase, Serine Carboxypeptidase, Protective Protein, Glycoprotein, Zymogen
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. Rudenko, E. Bonten, A. D'Azzo, W. G. Hol
Three-Dimensional Structure Of The Human 'Protective Protein': Structure Of The Precursor Form Suggests A Comple Activation Mechanism.
Structure V. 3 1249 1995
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 6)
Info
All Hetero Components
1a: N-ACETYL-D-GLUCOSAMINE (NAGa)
1b: N-ACETYL-D-GLUCOSAMINE (NAGb)
1c: N-ACETYL-D-GLUCOSAMINE (NAGc)
1d: N-ACETYL-D-GLUCOSAMINE (NAGd)
1e: N-ACETYL-D-GLUCOSAMINE (NAGe)
2a: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAG
5
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
2
NDG
1
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
[
close Hetero Component info
]
Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: CAT (UNKNOWN)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASN A:117 , GLU A:120 , ARG A:343 , LEU A:345 , NDG A:3011 , GLN B:4
BINDING SITE FOR RESIDUE NAG A 3010
2
AC2
SOFTWARE
NAG A:3010
BINDING SITE FOR RESIDUE NDG A 3011
3
AC3
SOFTWARE
PRO A:77 , ASN A:305 , THR A:307 , HOH A:3028
BINDING SITE FOR RESIDUE NAG A 3020
4
AC4
SOFTWARE
ASN B:117 , LEU B:345 , NAG B:3031
BINDING SITE FOR RESIDUE NAG B 3030
5
AC5
SOFTWARE
NAG B:3030
BINDING SITE FOR RESIDUE NAG B 3031
6
AC6
SOFTWARE
PRO B:77 , ASN B:305
BINDING SITE FOR RESIDUE NAG B 3040
7
CAT
UNKNOWN
SER A:150 , ASP A:372 , HIS A:429 , SER B:150 , ASP B:372 , HIS B:429
CATALYTIC TRIAD SERINE CARBOXYPEPTIDASE.
[
close Site info
]
SAPs(SNPs)/Variants
(12, 24)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_001385 (Q21R, chain A/B, )
02: VAR_063018 (S23Y, chain A/B, )
03: VAR_001386 (W37R, chain A/B, )
04: VAR_001387 (S62L, chain A/B, )
05: VAR_063019 (V104M, chain A/B, )
06: VAR_063020 (L208P, chain A/B, )
07: VAR_001388 (Y221N, chain A/B, )
08: VAR_001389 (Y367C, chain A/B, )
09: VAR_063021 (M378T, chain A/B, )
10: VAR_063022 (G411S, chain A/B, )
11: VAR_001390 (F412V, chain A/B, )
12: VAR_063023 (K425E, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_001385
Q
49
R
PPGB_HUMAN
Disease (GSL)
---
A/B
Q
21
R
02
UniProt
VAR_063018
S
51
Y
PPGB_HUMAN
Disease (GSL)
---
A/B
S
23
Y
03
UniProt
VAR_001386
W
65
R
PPGB_HUMAN
Disease (GSL)
28934603
A/B
W
37
R
04
UniProt
VAR_001387
S
90
L
PPGB_HUMAN
Disease (GSL)
---
A/B
S
62
L
05
UniProt
VAR_063019
V
132
M
PPGB_HUMAN
Disease (GSL)
---
A/B
V
104
M
06
UniProt
VAR_063020
L
236
P
PPGB_HUMAN
Disease (GSL)
---
A/B
L
208
P
07
UniProt
VAR_001388
Y
249
N
PPGB_HUMAN
Disease (GSL)
---
A/B
Y
221
N
08
UniProt
VAR_001389
Y
395
C
PPGB_HUMAN
Disease (GSL)
---
A/B
Y
367
C
09
UniProt
VAR_063021
M
406
T
PPGB_HUMAN
Disease (GSL)
---
A/B
M
378
T
10
UniProt
VAR_063022
G
439
S
PPGB_HUMAN
Disease (GSL)
---
A/B
G
411
S
11
UniProt
VAR_001390
F
440
V
PPGB_HUMAN
Disease (GSL)
---
A/B
F
412
V
12
UniProt
VAR_063023
K
453
E
PPGB_HUMAN
Disease (GSL)
---
A/B
K
425
E
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: CARBOXYPEPT_SER_SER (A:146-153,B:146-153)
2: CARBOXYPEPT_SER_HIS (A:419-436,B:419-436)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CARBOXYPEPT_SER_SER
PS00131
Serine carboxypeptidases, serine active site.
PPGB_HUMAN
174-181
2
A:146-153
B:146-153
2
CARBOXYPEPT_SER_HIS
PS00560
Serine carboxypeptidases, histidine active site.
PPGB_HUMAN
447-464
2
A:419-436
B:419-436
[
close PROSITE info
]
Exons
(8, 16)
Info
All Exons
Exon 1.2e (A:1-37 | B:1-37)
Exon 1.3 (A:37-74 | B:37-74)
Exon 1.4a (A:75-91 | B:75-91)
Exon 1.5 (A:92-120 | B:92-120)
Exon 1.6 (A:121-172 | B:121-172)
Exon 1.7b (A:173-203 | B:173-203)
Exon 1.8a (A:203-231 | B:203-231)
Exon 1.9b (A:232-261 | B:232-261 (gaps))
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.2e
2: Boundary 1.2e/1.3
3: Boundary 1.3/1.4a
4: Boundary 1.4a/1.5
5: Boundary 1.5/1.6
6: Boundary 1.6/1.7b
7: Boundary 1.7b/1.8a
8: Boundary 1.8a/1.9b
9: 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
1.2e
ENST00000372459
2e
ENSE00001457871
chr20:
44520053-44520401
349
PPGB_HUMAN
1-65
65
2
A:1-37
B:1-37
37
37
1.3
ENST00000372459
3
ENSE00000662429
chr20:
44520555-44520666
112
PPGB_HUMAN
65-102
38
2
A:37-74
B:37-74
38
38
1.4a
ENST00000372459
4a
ENSE00000845061
chr20:
44520912-44520962
51
PPGB_HUMAN
103-119
17
2
A:75-91
B:75-91
17
17
1.5
ENST00000372459
5
ENSE00000845062
chr20:
44521037-44521123
87
PPGB_HUMAN
120-148
29
2
A:92-120
B:92-120
29
29
1.6
ENST00000372459
6
ENSE00000845063
chr20:
44521364-44521519
156
PPGB_HUMAN
149-200
52
2
A:121-172
B:121-172
52
52
1.7b
ENST00000372459
7b
ENSE00000662432
chr20:
44521859-44521950
92
PPGB_HUMAN
201-231
31
2
A:173-203
B:173-203
31
31
1.8a
ENST00000372459
8a
ENSE00000662433
chr20:
44522627-44522711
85
PPGB_HUMAN
231-259
29
2
A:203-231
B:203-231
29
29
1.9b
ENST00000372459
9b
ENSE00002189764
chr20:
44523289-44523380
92
PPGB_HUMAN
260-289
30
2
A:232-261
B:232-261 (gaps)
30
30
[
close EXON info
]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1ivya_ (A:)
1b: SCOP_d1ivyb_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
alpha/beta-Hydrolases
(971)
Superfamily
:
alpha/beta-Hydrolases
(971)
Family
:
Serine carboxypeptidase-like
(15)
Protein domain
:
Human 'protective protein', HPP
(4)
Human (Homo sapiens) [TaxId: 9606]
(4)
1a
d1ivya_
A:
1b
d1ivyb_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1ivyB00 (B:1-452)
1b: CATH_1ivyA00 (A:1-452)
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=3.40.50.1820, no name defined]
(692)
Human (Homo sapiens)
(118)
1a
1ivyB00
B:1-452
1b
1ivyA00
A:1-452
[
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 (159 KB)
Header - Asym.Unit
Biol.Unit 1 (153 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
1IVY
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
