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.
5CCJ
Biol. Unit 5
Info
Asym.Unit (253 KB)
Biol.Unit 1 (65 KB)
Biol.Unit 2 (67 KB)
Biol.Unit 3 (61 KB)
Biol.Unit 4 (65 KB)
Biol.Unit 5 (245 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 QUINTUPLE MUTANT OF THE SYNAPTOTAGMIN-1 C2B DOMAIN
Authors
:
Q. Zhou, M. Zhao, A. T. Brunger
Date
:
02 Jul 15 (Deposition) - 12 Aug 15 (Release) - 16 Sep 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.65
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Biol. Unit 5: A,B,C,D (1x)
Keywords
:
Synaptotagmin1, C2B Domain, Signaling Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Q. Zhou, Y. Lai, T. Bacaj, M. Zhao, A. Y. Lyubimov, M. Uervirojnangkoorn, O. B. Zeldin, A. S. Brewster, N. K. Sauter, A. E. Cohen, S. M. Soltis, R. Alonso-Mori, M. Chollet, H. T. Lemke, R. A. Pfuetzner, U. B. Choi, W. I. Weis, J. Diao, T. C. Sudhof, A. T. Brunger
Architecture Of The Synaptotagmin-Snare Machinery For Neuronal Exocytosis.
Nature V. 525 62 2015
[
close entry info
]
Hetero Components
(2, 49)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1aa: GLYCEROL (GOLaa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
1d: GLYCEROL (GOLd)
1e: GLYCEROL (GOLe)
1f: GLYCEROL (GOLf)
1g: GLYCEROL (GOLg)
1h: GLYCEROL (GOLh)
1i: GLYCEROL (GOLi)
1j: GLYCEROL (GOLj)
1k: GLYCEROL (GOLk)
1l: GLYCEROL (GOLl)
1m: GLYCEROL (GOLm)
1n: GLYCEROL (GOLn)
1o: GLYCEROL (GOLo)
1p: GLYCEROL (GOLp)
1q: GLYCEROL (GOLq)
1r: GLYCEROL (GOLr)
1s: GLYCEROL (GOLs)
1t: GLYCEROL (GOLt)
1u: GLYCEROL (GOLu)
1v: GLYCEROL (GOLv)
1w: GLYCEROL (GOLw)
1x: GLYCEROL (GOLx)
1y: GLYCEROL (GOLy)
1z: GLYCEROL (GOLz)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
2d: SULFATE ION (SO4d)
2e: SULFATE ION (SO4e)
2f: SULFATE ION (SO4f)
2g: SULFATE ION (SO4g)
2h: SULFATE ION (SO4h)
2i: SULFATE ION (SO4i)
2j: SULFATE ION (SO4j)
2k: SULFATE ION (SO4k)
2l: SULFATE ION (SO4l)
2m: SULFATE ION (SO4m)
2n: SULFATE ION (SO4n)
2o: SULFATE ION (SO4o)
2p: SULFATE ION (SO4p)
2q: SULFATE ION (SO4q)
2r: SULFATE ION (SO4r)
2s: SULFATE ION (SO4s)
2t: SULFATE ION (SO4t)
2u: SULFATE ION (SO4u)
2v: SULFATE ION (SO4v)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
27
Ligand/Ion
GLYCEROL
2
SO4
22
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(49, 49)
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)
36: AF9 (SOFTWARE)
37: AG1 (SOFTWARE)
38: AG2 (SOFTWARE)
39: AG3 (SOFTWARE)
40: AG4 (SOFTWARE)
41: AG5 (SOFTWARE)
42: AG6 (SOFTWARE)
43: AG7 (SOFTWARE)
44: AG8 (SOFTWARE)
45: AG9 (SOFTWARE)
46: AH1 (SOFTWARE)
47: AH2 (SOFTWARE)
48: AH3 (SOFTWARE)
49: AH4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR A:383 , GLY A:384 , HOH A:616 , HOH A:765 , LEU C:294 , ASN C:340 , SO4 C:507 , HOH C:729 , ALA D:395 , ASN D:396
binding site for residue GOL A 501
02
AC2
SOFTWARE
TYR A:311 , LYS A:327 , THR A:328 , ILE A:330 , SO4 A:508 , HOH A:608 , HOH A:651
binding site for residue GOL A 502
03
AC3
SOFTWARE
THR A:334 , LEU A:335 , ASN A:336 , HOH A:609 , HOH A:641 , HOH A:696 , HOH D:642 , HOH D:695
binding site for residue GOL A 503
04
AC4
SOFTWARE
VAL A:376 , PHE A:377 , SER A:382 , THR A:383 , GLU A:386 , MET A:416
binding site for residue GOL A 504
05
AC5
SOFTWARE
ARG A:322 , LYS A:325 , SO4 A:507 , HOH A:723
binding site for residue GOL A 505
06
AC6
SOFTWARE
ALA A:399 , PRO A:400 , HOH A:615 , HOH A:714 , ARG B:388 , SER B:391 , ASP B:392 , SO4 B:510 , HOH B:717 , HOH C:650
binding site for residue GOL A 506
07
AC7
SOFTWARE
LYS A:313 , HIS A:315 , ARG A:322 , LYS A:325 , GOL A:505 , HOH A:612
binding site for residue SO4 A 507
08
AC8
SOFTWARE
TYR A:311 , LYS A:313 , LYS A:325 , LYS A:327 , ASN A:370 , GOL A:502 , HOH A:607
binding site for residue SO4 A 508
09
AC9
SOFTWARE
TRP A:338 , ASN A:340 , HOH A:680 , GOL C:504 , LYS D:354 , LYS D:420
binding site for residue SO4 A 509
10
AD1
SOFTWARE
ARG A:322
binding site for residue SO4 A 510
11
AD2
SOFTWARE
LYS A:300 , HOH A:604 , ILE B:330 , TYR B:364
binding site for residue SO4 A 511
12
AD3
SOFTWARE
LYS A:369 , LYS B:326 , HOH B:623 , HOH B:646
binding site for residue GOL B 501
13
AD4
SOFTWARE
LYS B:327 , THR B:328 , ILE B:330 , SO4 B:512 , HOH B:604 , HOH B:622
binding site for residue GOL B 502
14
AD5
SOFTWARE
ASN B:340 , SER B:342 , HOH B:614 , HOH B:698 , HOH B:720 , HOH B:734 , ALA C:395 , GOL D:505
binding site for residue GOL B 503
15
AD6
SOFTWARE
LYS B:324 , LYS B:326 , SER B:344 , PHE B:345 , GLU B:346 , HOH B:719 , HOH B:737
binding site for residue GOL B 504
16
AD7
SOFTWARE
THR B:329 , ILE B:330 , HOH B:622 , HOH B:627
binding site for residue GOL B 505
17
AD8
SOFTWARE
ARG B:388 , SO4 B:513 , HOH B:611 , HOH B:631 , HOH B:652 , HOH B:727
binding site for residue GOL B 506
18
AD9
SOFTWARE
TRP B:338 , ASN B:340 , HOH B:724 , PRO C:397
binding site for residue GOL B 507
19
AE1
SOFTWARE
HOH A:603 , HOH A:624 , LYS B:313 , HIS B:315 , ARG B:322 , LYS B:325 , HOH B:742
binding site for residue SO4 B 508
20
AE2
SOFTWARE
LYS B:321 , ARG B:322 , LYS B:421 , HOH B:741
binding site for residue SO4 B 509
21
AE3
SOFTWARE
GOL A:506 , ARG B:388 , GLN B:403 , HOH B:608 , HOH B:631 , HOH B:658 , HOH B:670 , TYR C:380 , HOH C:673
binding site for residue SO4 B 510
22
AE4
SOFTWARE
THR B:334 , LEU B:335 , ASN B:336
binding site for residue SO4 B 511
23
AE5
SOFTWARE
ASP A:303 , VAL A:304 , HOH A:603 , TYR B:311 , LYS B:313 , LYS B:325 , LYS B:327 , GOL B:502 , HOH B:604
binding site for residue SO4 B 512
24
AE6
SOFTWARE
GLY B:384 , ARG B:388 , GOL B:506 , HOH B:620 , GOL D:502 , HOH D:607
binding site for residue SO4 B 513
25
AE7
SOFTWARE
GLY B:368 , LYS B:369 , HOH B:628
binding site for residue SO4 B 514
26
AE8
SOFTWARE
LYS B:331 , LYS B:332 , HOH B:627 , HOH B:630 , HOH B:707 , HOH B:728
binding site for residue SO4 B 515
27
AE9
SOFTWARE
VAL C:376 , PHE C:377 , SER C:382 , THR C:383 , GLU C:386 , HOH C:603
binding site for residue GOL C 501
28
AF1
SOFTWARE
HOH B:606 , THR C:334 , LEU C:335 , ASN C:336 , HOH C:605
binding site for residue GOL C 502
29
AF2
SOFTWARE
LYS C:331 , LYS C:332 , HOH C:602 , HOH C:634 , HOH C:639 , HOH C:642
binding site for residue GOL C 503
30
AF3
SOFTWARE
LEU A:294 , ASN A:340 , SO4 A:509 , HOH A:742 , HOH A:752 , ALA B:395 , ASN B:396 , THR C:383 , GLY C:384
binding site for residue GOL C 504
31
AF4
SOFTWARE
ARG C:322 , LEU C:323 , LYS C:324 , LYS C:325
binding site for residue GOL C 505
32
AF5
SOFTWARE
TYR C:311 , LYS C:313 , ASN C:370 , HOH C:641 , ILE D:367 , GLY D:368
binding site for residue GOL C 506
33
AF6
SOFTWARE
GOL A:501 , HOH A:778 , LYS B:354 , LYS B:420 , TRP C:338 , ASN C:340 , HOH C:606
binding site for residue SO4 C 507
34
AF7
SOFTWARE
LYS C:313 , HIS C:315
binding site for residue SO4 C 508
35
AF8
SOFTWARE
LYS C:321 , ARG C:322
binding site for residue SO4 C 509
36
AF9
SOFTWARE
LYS D:327 , THR D:328 , ILE D:330 , ASN D:370 , HOH D:715
binding site for residue GOL D 501
37
AG1
SOFTWARE
ALA A:395 , THR B:383 , GLY B:384 , SO4 B:513 , HOH B:702 , GOL D:504 , GOL D:508 , HOH D:607 , HOH D:719
binding site for residue GOL D 502
38
AG2
SOFTWARE
ALA B:286 , GLU D:412 , MET D:416 , HOH D:616 , HOH D:767
binding site for residue GOL D 503
39
AG3
SOFTWARE
ALA A:395 , HOH A:795 , VAL D:292 , ASN D:340 , SER D:342 , GOL D:502 , HOH D:669 , HOH D:676
binding site for residue GOL D 504
40
AG4
SOFTWARE
GOL B:503 , HOH B:698 , THR D:383 , HOH D:627 , HOH D:646 , HOH D:660 , HOH D:661 , HOH D:746 , HOH D:751
binding site for residue GOL D 505
41
AG5
SOFTWARE
TRP D:338 , ASN D:340
binding site for residue GOL D 506
42
AG6
SOFTWARE
TYR A:380 , ASN A:381 , SER A:382 , HOH A:737 , ASP D:392 , HOH D:636 , HOH D:683 , HOH D:690 , HOH D:699 , HOH D:783
binding site for residue GOL D 507
43
AG7
SOFTWARE
HOH A:635 , HOH A:795 , THR B:383 , GOL D:502 , HOH D:633 , HOH D:640 , HOH D:665 , HOH D:669
binding site for residue GOL D 508
44
AG8
SOFTWARE
TYR A:380 , ARG D:388 , GLN D:403 , HOH D:602 , HOH D:636 , HOH D:658 , HOH D:711 , HOH D:738
binding site for residue SO4 D 509
45
AG9
SOFTWARE
LYS D:313 , HIS D:315 , ARG D:322 , LYS D:325
binding site for residue SO4 D 510
46
AH1
SOFTWARE
TYR D:311 , LYS D:313 , LYS D:325 , LYS D:327 , ASN D:370 , HOH D:612
binding site for residue SO4 D 511
47
AH2
SOFTWARE
THR D:334 , LEU D:335 , ASN D:336
binding site for residue SO4 D 512
48
AH3
SOFTWARE
LYS D:321 , ARG D:322 , LYS D:421
binding site for residue SO4 D 513
49
AH4
SOFTWARE
GLY D:384 , ARG D:388 , HOH D:608 , HOH D:661 , HOH D:667 , HOH D:689
binding site for residue SO4 D 514
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(, 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.
(no "Exon" information available for biological units yet)
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
Chain C
Chain D
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 (253 KB)
Header - Asym.Unit
Biol.Unit 1 (65 KB)
Header - Biol.Unit 1
Biol.Unit 2 (67 KB)
Header - Biol.Unit 2
Biol.Unit 3 (61 KB)
Header - Biol.Unit 3
Biol.Unit 4 (65 KB)
Header - Biol.Unit 4
Biol.Unit 5 (245 KB)
Header - Biol.Unit 5
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
5CCJ
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help