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.
5DI0
Asym. Unit
Info
Asym.Unit (131 KB)
Biol.Unit 1 (124 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 DLN1
Authors
:
N. Jia, Y. L. Jiang, W. Cheng, H. W. Wang, C. Z. Zhou, Y. Chen
Date
:
31 Aug 15 (Deposition) - 03 Feb 16 (Release) - 30 Mar 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.70
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Pore-Forming Protein, Aeolysin-Like Protein, Vetebrate, High-Mannose Glycans, Complex, Sugar Binding Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. Jia, N. Liu, W. Cheng, Y. L. Jiang, H. Sun, L. L. Chen, J. Peng, Y. Zhang Y. H. Ding, Z. H. Zhang, X. Wang, G. Cai, J. Wang, M. Q. Dong, Z. Zhang, H. Wu, H. W. Wang, Y. Chen, C. Z. Zhou
Structural Basis For Receptor Recognition And Pore Formatio Of A Zebrafish Aerolysin-Like Protein.
Embo Rep. V. 17 235 2016
[
close entry info
]
Hetero Components
(5, 35)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
2f: 1,2-ETHANEDIOL (EDOf)
2g: 1,2-ETHANEDIOL (EDOg)
2h: 1,2-ETHANEDIOL (EDOh)
2i: 1,2-ETHANEDIOL (EDOi)
2j: 1,2-ETHANEDIOL (EDOj)
2k: 1,2-ETHANEDIOL (EDOk)
2l: 1,2-ETHANEDIOL (EDOl)
3a: DI(HYDROXYETHYL)ETHER (PEGa)
3b: DI(HYDROXYETHYL)ETHER (PEGb)
3c: DI(HYDROXYETHYL)ETHER (PEGc)
3d: DI(HYDROXYETHYL)ETHER (PEGd)
3e: DI(HYDROXYETHYL)ETHER (PEGe)
3f: DI(HYDROXYETHYL)ETHER (PEGf)
3g: DI(HYDROXYETHYL)ETHER (PEGg)
3h: DI(HYDROXYETHYL)ETHER (PEGh)
4a: TETRAETHYLENE GLYCOL (PG4a)
4b: TETRAETHYLENE GLYCOL (PG4b)
4c: TETRAETHYLENE GLYCOL (PG4c)
4d: TETRAETHYLENE GLYCOL (PG4d)
4e: TETRAETHYLENE GLYCOL (PG4e)
4f: TETRAETHYLENE GLYCOL (PG4f)
5a: TRIETHYLENE GLYCOL (PGEa)
5b: TRIETHYLENE GLYCOL (PGEb)
5c: TRIETHYLENE GLYCOL (PGEc)
5d: TRIETHYLENE GLYCOL (PGEd)
5e: TRIETHYLENE GLYCOL (PGEe)
5f: TRIETHYLENE GLYCOL (PGEf)
5g: TRIETHYLENE GLYCOL (PGEg)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
2
Ligand/Ion
CHLORIDE ION
2
EDO
12
Ligand/Ion
1,2-ETHANEDIOL
3
PEG
8
Ligand/Ion
DI(HYDROXYETHYL)ETHER
4
PG4
6
Ligand/Ion
TETRAETHYLENE GLYCOL
5
PGE
7
Ligand/Ion
TRIETHYLENE GLYCOL
[
close Hetero Component info
]
Sites
(35, 35)
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: AD1 (SOFTWARE)
11: AD2 (SOFTWARE)
12: AD3 (SOFTWARE)
13: AD4 (SOFTWARE)
14: AD5 (SOFTWARE)
15: AD6 (SOFTWARE)
16: AD7 (SOFTWARE)
17: AD8 (SOFTWARE)
18: AD9 (SOFTWARE)
19: AE1 (SOFTWARE)
20: AE2 (SOFTWARE)
21: AE3 (SOFTWARE)
22: AE4 (SOFTWARE)
23: AE5 (SOFTWARE)
24: AE6 (SOFTWARE)
25: AE7 (SOFTWARE)
26: AE8 (SOFTWARE)
27: AE9 (SOFTWARE)
28: AF1 (SOFTWARE)
29: AF2 (SOFTWARE)
30: AF3 (SOFTWARE)
31: AF4 (SOFTWARE)
32: AF5 (SOFTWARE)
33: AF6 (SOFTWARE)
34: AF7 (SOFTWARE)
35: AF8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
VAL A:36 , THR A:106 , HOH A:522 , HOH A:563 , HOH A:744 , HOH A:755 , HOH A:762 , GLU B:100 , PG4 B:416 , HOH B:511
binding site for residue EDO A 401
02
AC2
SOFTWARE
LEU A:7 , PEG A:408 , HOH A:511 , HOH A:547
binding site for residue EDO A 402
03
AC3
SOFTWARE
ILE A:10 , GLY A:11 , TYR A:114 , EDO A:404 , CL A:418
binding site for residue EDO A 403
04
AC4
SOFTWARE
ILE A:9 , GLY A:11 , GLY A:12 , EDO A:403 , EDO A:405 , PEG A:408
binding site for residue EDO A 404
05
AC5
SOFTWARE
GLY A:11 , GLN A:13 , GLY A:85 , EDO A:404
binding site for residue EDO A 405
06
AC6
SOFTWARE
SER A:16 , PHE A:18 , PHE A:56 , GLY A:57 , GLY A:130 , HOH A:501 , HOH A:504 , HOH A:508 , HOH A:576 , HOH A:720
binding site for residue PEG A 406
07
AC7
SOFTWARE
GLY A:38 , TRP A:39 , SER A:107 , HOH A:506 , HOH A:554 , GLY B:109
binding site for residue PEG A 407
08
AC8
SOFTWARE
SER A:17 , VAL A:127 , GLY A:128 , ARG A:129 , EDO A:402 , EDO A:404
binding site for residue PEG A 408
09
AC9
SOFTWARE
ASN A:24 , ASN A:25 , ASP A:50 , ARG A:52 , HOH A:503 , HOH A:654 , HOH A:688 , HOH A:734 , THR B:157
binding site for residue PEG A 409
10
AD1
SOFTWARE
ASN A:25 , GLY A:26 , SER A:49 , THR A:202 , PHE A:205 , HOH A:524
binding site for residue PEG A 410
11
AD2
SOFTWARE
THR A:167 , GLU A:222 , THR A:266 , ILE A:267 , GLY A:268 , LYS A:307 , ASN A:309 , HOH A:517 , HOH A:569
binding site for residue PEG A 411
12
AD3
SOFTWARE
THR A:5 , ASN A:6 , LEU A:7 , GLU A:8 , HOH A:547 , HOH A:606 , HOH A:727 , HOH A:779
binding site for residue PGE A 412
13
AD4
SOFTWARE
ARG A:87 , GLY A:131 , SER A:132 , ASP A:133 , ASP A:135
binding site for residue PGE A 413
14
AD5
SOFTWARE
GLY A:71 , ASN A:96 , LYS A:97
binding site for residue PGE A 414
15
AD6
SOFTWARE
HIS A:104 , MET A:105 , SER A:107 , TRP A:108 , HOH A:545 , HOH A:678
binding site for residue PGE A 415
16
AD7
SOFTWARE
TRP A:80 , LYS A:92 , LYS A:94 , GLU A:100 , PHE A:102 , GLU A:113 , HOH A:534
binding site for residue PG4 A 416
17
AD8
SOFTWARE
GLU A:30 , LYS A:31 , TRP A:47 , VAL A:67 , HOH A:681 , EDO B:407
binding site for residue PG4 A 417
18
AD9
SOFTWARE
GLY A:81 , GLY A:83 , GLY A:85 , EDO A:403 , HOH A:739
binding site for residue CL A 418
19
AE1
SOFTWARE
PHE B:18 , VAL B:127 , GLY B:128
binding site for residue EDO B 401
20
AE2
SOFTWARE
ILE B:10 , GLY B:11 , EDO B:403 , CL B:417
binding site for residue EDO B 402
21
AE3
SOFTWARE
GLY B:11 , GLN B:13 , EDO B:402 , HOH B:867
binding site for residue EDO B 403
22
AE4
SOFTWARE
GLU B:184 , HOH B:545 , HOH B:620 , HOH B:862
binding site for residue EDO B 404
23
AE5
SOFTWARE
ASN B:25 , SER B:49 , ASP B:50 , THR B:202 , HOH B:506 , HOH B:818
binding site for residue EDO B 405
24
AE6
SOFTWARE
THR A:69 , PG4 B:414
binding site for residue EDO B 406
25
AE7
SOFTWARE
PG4 A:417 , THR B:69 , GLU B:72 , LYS B:97 , HOH B:580 , HOH B:617
binding site for residue EDO B 407
26
AE8
SOFTWARE
THR B:5 , ASN B:6 , LEU B:7 , GLU B:8 , HOH B:504 , HOH B:609
binding site for residue PEG B 408
27
AE9
SOFTWARE
THR B:167 , THR B:266 , ILE B:267 , GLY B:268 , LYS B:307 , HOH B:517 , HOH B:772
binding site for residue PEG B 409
28
AF1
SOFTWARE
SER B:16 , PHE B:18 , GLU B:54 , PHE B:56 , GLY B:57 , GLY B:130 , HOH B:547
binding site for residue PGE B 410
29
AF2
SOFTWARE
HIS B:104 , MET B:105 , SER B:107 , TRP B:108 , HOH B:744 , HOH B:775
binding site for residue PGE B 411
30
AF3
SOFTWARE
SER A:107 , HOH A:584 , TRP B:39 , TRP B:108 , HOH B:648 , HOH B:754 , HOH B:771
binding site for residue PGE B 412
31
AF4
SOFTWARE
ARG B:87 , GLY B:131 , SER B:132 , ASP B:133 , ASP B:135 , HOH B:549 , HOH B:769
binding site for residue PG4 B 413
32
AF5
SOFTWARE
LYS B:31 , TRP B:47 , EDO B:406 , HOH B:654 , HOH B:675
binding site for residue PG4 B 414
33
AF6
SOFTWARE
LYS A:191 , PRO B:70 , ASN B:96 , LYS B:97 , HOH B:580
binding site for residue PG4 B 415
34
AF7
SOFTWARE
EDO A:401 , SER B:76 , LEU B:77 , TRP B:80 , LYS B:92 , LYS B:94 , GLU B:100 , PHE B:102 , GLU B:113
binding site for residue PG4 B 416
35
AF8
SOFTWARE
GLY B:81 , ASN B:82 , GLY B:83 , GLY B:85 , EDO B:402 , HOH B:845
binding site for residue CL B 417
[
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
(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 (131 KB)
Header - Asym.Unit
Biol.Unit 1 (124 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
5DI0
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
