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...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
4F8Z
Asym. Unit
Info
Asym.Unit (141 KB)
Biol.Unit 1 (135 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CARBOXYPEPTIDASE T WITH BOC-LEU
Authors
:
V. I. Timofeev, S. A. Kuznetsov, V. K. Akparov, I. P. Kuranova
Date
:
18 May 12 (Deposition) - 22 May 13 (Release) - 30 Sep 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.38
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
V. I. Timofeev, S. A. Kuznetsov, V. K. H. Akparov, G. G. Chestukhina, I. P. Kuranova
Three-Dimensional Structure Of Carboxypeptidase T From Thermoactinomyces Vulgaris In Complex With N-Boc-L-Leucine.
Biochemistry Mosc. V. 78 252 2013
[
close entry info
]
Hetero Components
(5, 31)
Info
All Hetero Components
1a: N-(TERT-BUTOXYCARBONYL)-L-LEUCINE (BL2a)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
2d: CALCIUM ION (CAd)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
3e: GLYCEROL (GOLe)
3f: GLYCEROL (GOLf)
3g: GLYCEROL (GOLg)
3h: GLYCEROL (GOLh)
3i: GLYCEROL (GOLi)
3j: GLYCEROL (GOLj)
3k: GLYCEROL (GOLk)
3l: GLYCEROL (GOLl)
3m: GLYCEROL (GOLm)
3n: GLYCEROL (GOLn)
3o: GLYCEROL (GOLo)
3p: GLYCEROL (GOLp)
3q: GLYCEROL (GOLq)
3r: GLYCEROL (GOLr)
3s: GLYCEROL (GOLs)
3t: GLYCEROL (GOLt)
3u: GLYCEROL (GOLu)
3v: GLYCEROL (GOLv)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
5a: ZINC ION (ZNa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BL2
1
Ligand/Ion
N-(TERT-BUTOXYCARBONYL)-L-LEUCINE
2
CA
4
Ligand/Ion
CALCIUM ION
3
GOL
22
Ligand/Ion
GLYCEROL
4
SO4
3
Ligand/Ion
SULFATE ION
5
ZN
1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(31, 31)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:69 , GLU A:72 , HIS A:204 , BL2 A:402
BINDING SITE FOR RESIDUE ZN A 401
02
AC2
SOFTWARE
HIS A:69 , ARG A:71 , GLU A:72 , ARG A:129 , HIS A:204 , THR A:205 , TYR A:206 , SER A:207 , TYR A:255 , GLU A:277 , PHE A:287 , ZN A:401 , SO4 A:403 , HOH A:507
BINDING SITE FOR RESIDUE BL2 A 402
03
AC3
SOFTWARE
HIS A:69 , ARG A:129 , ASN A:146 , ARG A:147 , TYR A:255 , GLU A:277 , BL2 A:402 , GOL A:413
BINDING SITE FOR RESIDUE SO4 A 403
04
AC4
SOFTWARE
PHE A:174 , ARG A:183 , ASN A:187 , TRP A:264 , GLN A:268 , HOH A:622 , HOH A:643 , HOH A:809
BINDING SITE FOR RESIDUE SO4 A 404
05
AC5
SOFTWARE
VAL A:16 , ASN A:20 , ASN A:25 , LYS A:32 , TRP A:45 , HOH A:533 , HOH A:841
BINDING SITE FOR RESIDUE SO4 A 405
06
AC6
SOFTWARE
SER A:50 , ASP A:51 , GLU A:57 , GLU A:59 , HOH A:506
BINDING SITE FOR RESIDUE CA A 406
07
AC7
SOFTWARE
ASP A:56 , GLU A:57 , GLU A:61 , GLU A:104 , HOH A:646 , HOH A:800
BINDING SITE FOR RESIDUE CA A 407
08
AC8
SOFTWARE
ASP A:51 , GLU A:57 , GLU A:59 , ASN A:101
BINDING SITE FOR RESIDUE CA A 408
09
AC9
SOFTWARE
SER A:7 , TYR A:9 , GLU A:14 , HOH A:501 , HOH A:555 , HOH A:866
BINDING SITE FOR RESIDUE CA A 409
10
BC1
SOFTWARE
PRO A:3 , SER A:4 , TYR A:5 , HOH A:759 , HOH A:781
BINDING SITE FOR RESIDUE GOL A 410
11
BC2
SOFTWARE
HIS A:10 , LYS A:18 , HOH A:603 , HOH A:675
BINDING SITE FOR RESIDUE GOL A 411
12
BC3
SOFTWARE
HIS A:10 , LYS A:18 , GLU A:77 , LEU A:80 , TYR A:81 , ASP A:84 , ILE A:294 , HOH A:634 , HOH A:758
BINDING SITE FOR RESIDUE GOL A 412
13
BC4
SOFTWARE
ASN A:146 , LEU A:211 , ALA A:251 , THR A:257 , ASP A:260 , SO4 A:403 , HOH A:737 , HOH A:810
BINDING SITE FOR RESIDUE GOL A 413
14
BC5
SOFTWARE
TRP A:128 , TYR A:140 , VAL A:141 , GOL A:415 , HOH A:552 , HOH A:589 , HOH A:623 , HOH A:693 , HOH A:726
BINDING SITE FOR RESIDUE GOL A 414
15
BC6
SOFTWARE
SER A:139 , TYR A:140 , GOL A:414
BINDING SITE FOR RESIDUE GOL A 415
16
BC7
SOFTWARE
PHE A:33 , ASP A:184 , PHE A:185 , GOL A:417 , HOH A:539 , HOH A:897
BINDING SITE FOR RESIDUE GOL A 416
17
BC8
SOFTWARE
LYS A:48 , TYR A:106 , GOL A:416 , HOH A:556
BINDING SITE FOR RESIDUE GOL A 417
18
BC9
SOFTWARE
GLY A:193 , GLN A:195 , HIS A:269 , HOH A:694 , HOH A:805 , HOH A:831
BINDING SITE FOR RESIDUE GOL A 418
19
CC1
SOFTWARE
VAL A:221 , PRO A:222 , SER A:223 , TYR A:283 , ASN A:284 , PRO A:285 , GOL A:421 , HOH A:518 , HOH A:580 , HOH A:630 , HOH A:682
BINDING SITE FOR RESIDUE GOL A 419
20
CC2
SOFTWARE
THR A:226 , GLN A:227 , ASP A:228 , HOH A:820 , HOH A:833 , HOH A:890
BINDING SITE FOR RESIDUE GOL A 420
21
CC3
SOFTWARE
SER A:223 , TYR A:288 , GOL A:419 , HOH A:585 , HOH A:587 , HOH A:630 , HOH A:801 , HOH A:862
BINDING SITE FOR RESIDUE GOL A 421
22
CC4
SOFTWARE
SER A:138 , SER A:139 , TYR A:140 , ARG A:171 , SER A:172 , HOH A:547 , HOH A:620
BINDING SITE FOR RESIDUE GOL A 422
23
CC5
SOFTWARE
TYR A:39 , GLN A:133 , PRO A:134 , ARG A:171 , GOL A:427 , HOH A:685 , HOH A:742 , HOH A:826
BINDING SITE FOR RESIDUE GOL A 423
24
CC6
SOFTWARE
ARG A:296 , SER A:299 , HOH A:772 , HOH A:799
BINDING SITE FOR RESIDUE GOL A 424
25
CC7
SOFTWARE
ASP A:1 , ASN A:11 , GLU A:117 , ILE A:120 , HOH A:548 , HOH A:701 , HOH A:881
BINDING SITE FOR RESIDUE GOL A 425
26
CC8
SOFTWARE
SER A:207 , THR A:247 , THR A:281 , HOH A:669 , HOH A:806
BINDING SITE FOR RESIDUE GOL A 426
27
CC9
SOFTWARE
PHE A:174 , SER A:175 , PRO A:177 , ALA A:180 , GOL A:423 , HOH A:566 , HOH A:826 , HOH A:851
BINDING SITE FOR RESIDUE GOL A 427
28
DC1
SOFTWARE
THR A:239 , TYR A:307 , LYS A:311 , HOH A:787 , HOH A:843
BINDING SITE FOR RESIDUE GOL A 428
29
DC2
SOFTWARE
TYR A:12 , ARG A:42 , GLU A:117 , GOL A:431
BINDING SITE FOR RESIDUE GOL A 429
30
DC3
SOFTWARE
TYR A:81 , ASP A:84 , LEU A:85 , GLN A:88 , ASN A:89 , HOH A:818 , HOH A:840
BINDING SITE FOR RESIDUE GOL A 430
31
DC4
SOFTWARE
GLU A:40 , GLY A:41 , GOL A:429
BINDING SITE FOR RESIDUE GOL A 431
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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
(1, 1)
Info
All SCOP Domains
1a: SCOP_d4f8za_ (A:)
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
:
Carboxypeptidase T
(12)
Protein domain
:
Carboxypeptidase T
(12)
Thermoactinomyces vulgaris [TaxId: 2026]
(12)
1a
d4f8za_
A:
[
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
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 (141 KB)
Header - Asym.Unit
Biol.Unit 1 (135 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
4F8Z
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
