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.
2PCU
Asym. Unit
Info
Asym.Unit (63 KB)
Biol.Unit 1 (57 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
HUMAN CARBOXYPEPTIDASE A4 IN COMPLEX WITH A CLEAVED HEXAPEPTIDE.
Authors
:
A. Bayes, D. Fernandez, M. Sola, A. Marrero, S. Garcia-Pique, F. X. Avil J. Vendrell, F. X. Gomis-Ruth
Date
:
30 Mar 07 (Deposition) - 17 Apr 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.60
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Metallocarboxypeptidase; Metalloprotease; Product; Cleavage; Specificity; Human Carboxypeptidase A4, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Bayes, D. Fernandez, M. Sola, A. Marrero, S. Garcia-Pique, F. X. Aviles, J. Vendrell, F. X. Gomis-Ruth
Caught After The Act: A Human A-Type Metallocarboxypeptidas In A Product Complex With A Cleaved Hexapeptide.
Biochemistry V. 46 6921 2007
[
close entry info
]
Hetero Components
(5, 5)
Info
All Hetero Components
1a: ASPARTIC ACID (ASPa)
2a: GLYCEROL (GOLa)
3a: N-ACETYL-D-GLUCOSAMINE (NAGa)
4a: THIOCYANATE ION (SCNa)
5a: ZINC ION (ZNa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ASP
1
Mod. Amino Acid
ASPARTIC ACID
2
GOL
1
Ligand/Ion
GLYCEROL
3
NAG
1
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
4
SCN
1
Ligand/Ion
THIOCYANATE ION
5
ZN
1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(5, 5)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASN A:148 , HOH A:679
BINDING SITE FOR RESIDUE NAG A 901
2
AC2
SOFTWARE
HIS A:69 , GLU A:72 , HIS A:196 , VAL B:5
BINDING SITE FOR RESIDUE ZN A 999
3
AC3
SOFTWARE
LYS A:37 , THR A:54 , THR A:97 , GLU A:101 , HOH A:584 , HOH A:766
BINDING SITE FOR RESIDUE SCN A 502
4
AC4
SOFTWARE
HIS A:69 , ARG A:127 , ASN A:144 , ARG A:145 , HIS A:196 , MET A:203 , THR A:243 , VAL A:247 , TYR A:248 , THR A:268 , GLU A:270 , VAL B:5 , HOH B:556 , HOH B:605
BINDING SITE FOR RESIDUE ASP B 6
5
AC5
SOFTWARE
TRP A:73 , ARG A:124 , LEU A:280 , LEU A:281 , HOH A:548
BINDING SITE FOR RESIDUE GOL A 501
[
close Site info
]
SAPs(SNPs)/Variants
(3, 3)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_020393 (P46T, chain A, )
2: VAR_048595 (R71L, chain A, )
3: VAR_020394 (G191C, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_020393
P
157
T
CBPA4_HUMAN
Polymorphism
3735051
A
P
46
T
2
UniProt
VAR_048595
R
183
L
CBPA4_HUMAN
Polymorphism
3735053
A
R
71
L
3
UniProt
VAR_020394
G
303
C
CBPA4_HUMAN
Polymorphism
2171492
A
G
191
C
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: CARBOXYPEPT_ZN_1 (A:60-82)
2: CARBOXYPEPT_ZN_2 (A:196-206)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CARBOXYPEPT_ZN_1
PS00132
Zinc carboxypeptidases, zinc-binding region 1 signature.
CBPA4_HUMAN
172-194
1
A:60-82
2
CARBOXYPEPT_ZN_2
PS00133
Zinc carboxypeptidases, zinc-binding region 2 signature.
CBPA4_HUMAN
308-318
1
A:196-206
[
close PROSITE info
]
Exons
(8, 8)
Info
All Exons
Exon 1.6 (A:5-17)
Exon 1.7c (A:18-51)
Exon 1.8b (A:52-85)
Exon 1.9c (A:86-122)
Exon 1.10b (A:123-153)
Exon 1.11 (A:153-219)
Exon 1.12 (A:220-248)
Exon 1.13b (A:248-308)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.4a/1.6
2: Boundary 1.6/1.7c
3: Boundary 1.7c/1.8b
4: Boundary 1.8b/1.9c
5: Boundary 1.9c/1.10b
6: Boundary 1.10b/1.11
7: Boundary 1.11/1.12
8: Boundary 1.12/1.13b
9: Boundary 1.13b/-
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
ENST00000222482
1a
ENSE00001175329
chr7:
129932993-129933088
96
CBPA4_HUMAN
1-23
23
0
-
-
1.3
ENST00000222482
3
ENSE00000882290
chr7:
129938586-129938667
82
CBPA4_HUMAN
23-50
28
0
-
-
1.4a
ENST00000222482
4a
ENSE00000723226
chr7:
129939110-129939244
135
CBPA4_HUMAN
51-95
45
0
-
-
1.6
ENST00000222482
6
ENSE00000723228
chr7:
129940656-129940754
99
CBPA4_HUMAN
96-128
33
1
A:5-17
13
1.7c
ENST00000222482
7c
ENSE00000723230
chr7:
129944318-129944419
102
CBPA4_HUMAN
129-162
34
1
A:18-51
34
1.8b
ENST00000222482
8b
ENSE00000723233
chr7:
129945656-129945760
105
CBPA4_HUMAN
163-197
35
1
A:52-85
35
1.9c
ENST00000222482
9c
ENSE00000723234
chr7:
129946627-129946737
111
CBPA4_HUMAN
198-234
37
1
A:86-122
37
1.10b
ENST00000222482
10b
ENSE00000723236
chr7:
129948147-129948237
91
CBPA4_HUMAN
235-265
31
1
A:123-153
31
1.11
ENST00000222482
11
ENSE00000723239
chr7:
129950627-129950826
200
CBPA4_HUMAN
265-331
67
1
A:153-219
67
1.12
ENST00000222482
12
ENSE00000723240
chr7:
129951878-129951962
85
CBPA4_HUMAN
332-360
29
1
A:220-248
29
1.13b
ENST00000222482
13b
ENSE00001279439
chr7:
129962329-129964019
1691
CBPA4_HUMAN
360-421
62
1
A:248-308
61
[
close EXON info
]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d2pcua1 (A:5-307)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Phosphorylase/hydrolase-like
(558)
Superfamily
:
Zn-dependent exopeptidases
(214)
Family
:
Pancreatic carboxypeptidases
(77)
Protein domain
:
Carboxypeptidase A
(41)
Human (Homo sapiens) [TaxId: 9606]
(5)
1a
d2pcua1
A:5-307
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_Peptidase_M14_2pcuA01 (A:18-296)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Peptidase_MH
(119)
Family
:
Peptidase_M14
(33)
Homo sapiens (Human)
(5)
1a
Peptidase_M14-2pcuA01
A:18-296
[
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 (63 KB)
Header - Asym.Unit
Biol.Unit 1 (57 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
2PCU
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
