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.
4OIK
Biol. Unit 2
Info
Asym.Unit (124 KB)
Biol.Unit 1 (59 KB)
Biol.Unit 2 (56 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
(QUASI-)RACEMIC X-RAY CRYSTAL STRUCTURE OF GLYCOSYLATED CHEMOKINE SER-CCL1.
Authors
:
R. Okamoto, K. Mandal, M. R. Sawaya, Y. Kajihara, T. O. Yeates, S. B. H. Ke
Date
:
19 Jan 14 (Deposition) - 07 May 14 (Release) - 21 May 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Chemical Protein Synthesis, Quasi-Racemic Protein Crystallography, Glycoprotein, Chemokine, Signaling Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. Okamoto, K. Mandal, M. R. Sawaya, Y. Kajihara, T. O. Yeates, S. B. Ken
(Quasi-)Racemic X-Ray Structures Of Glycosylated And Non-Glycosylated Forms Of The Chemokine Ser-Ccl1 Prepared B Total Chemical Synthesis.
Angew. Chem. Int. Ed. Engl. V. 53 5194 2014
[
close entry info
]
Hetero Components
(21, 150)
Info
All Hetero Components
01a: CITRIC ACID (CITa)
01b: CITRIC ACID (CITb)
02a: D-ALANINE (DALa)
02b: D-ALANINE (DALb)
02c: D-ALANINE (DALc)
02d: D-ALANINE (DALd)
02e: D-ALANINE (DALe)
02f: D-ALANINE (DALf)
02g: D-ALANINE (DALg)
02h: D-ALANINE (DALh)
03a: D-ARGININE (DARa)
03b: D-ARGININE (DARb)
03c: D-ARGININE (DARc)
03d: D-ARGININE (DARd)
03e: D-ARGININE (DARe)
03f: D-ARGININE (DARf)
03g: D-ARGININE (DARg)
03h: D-ARGININE (DARh)
03i: D-ARGININE (DARi)
03j: D-ARGININE (DARj)
03k: D-ARGININE (DARk)
03l: D-ARGININE (DARl)
03m: D-ARGININE (DARm)
03n: D-ARGININE (DARn)
03o: D-ARGININE (DARo)
03p: D-ARGININE (DARp)
04a: D-ASPARTIC ACID (DASa)
04b: D-ASPARTIC ACID (DASb)
05a: D-CYSTEINE (DCYa)
05b: D-CYSTEINE (DCYb)
05c: D-CYSTEINE (DCYc)
05d: D-CYSTEINE (DCYd)
05e: D-CYSTEINE (DCYe)
05f: D-CYSTEINE (DCYf)
05g: D-CYSTEINE (DCYg)
05h: D-CYSTEINE (DCYh)
05i: D-CYSTEINE (DCYi)
05j: D-CYSTEINE (DCYj)
05k: D-CYSTEINE (DCYk)
05l: D-CYSTEINE (DCYl)
06a: D-GLUTAMIC ACID (DGLa)
06b: D-GLUTAMIC ACID (DGLb)
06c: D-GLUTAMIC ACID (DGLc)
06d: D-GLUTAMIC ACID (DGLd)
06e: D-GLUTAMIC ACID (DGLe)
06f: D-GLUTAMIC ACID (DGLf)
06g: D-GLUTAMIC ACID (DGLg)
06h: D-GLUTAMIC ACID (DGLh)
07a: D-GLUTAMINE (DGNa)
07b: D-GLUTAMINE (DGNb)
07c: D-GLUTAMINE (DGNc)
07d: D-GLUTAMINE (DGNd)
07e: D-GLUTAMINE (DGNe)
07f: D-GLUTAMINE (DGNf)
08a: D-HISTIDINE (DHIa)
08b: D-HISTIDINE (DHIb)
08c: D-HISTIDINE (DHIc)
08d: D-HISTIDINE (DHId)
09a: D-ISOLEUCINE (DILa)
09b: D-ISOLEUCINE (DILb)
09c: D-ISOLEUCINE (DILc)
09d: D-ISOLEUCINE (DILd)
09e: D-ISOLEUCINE (DILe)
09f: D-ISOLEUCINE (DILf)
09g: D-ISOLEUCINE (DILg)
09h: D-ISOLEUCINE (DILh)
10a: D-LEUCINE (DLEa)
10b: D-LEUCINE (DLEb)
10c: D-LEUCINE (DLEc)
10d: D-LEUCINE (DLEd)
10e: D-LEUCINE (DLEe)
10f: D-LEUCINE (DLEf)
10g: D-LEUCINE (DLEg)
10h: D-LEUCINE (DLEh)
10i: D-LEUCINE (DLEi)
10j: D-LEUCINE (DLEj)
10k: D-LEUCINE (DLEk)
10l: D-LEUCINE (DLEl)
11a: D-LYSINE (DLYa)
11b: D-LYSINE (DLYb)
11c: D-LYSINE (DLYc)
11d: D-LYSINE (DLYd)
11e: D-LYSINE (DLYe)
11f: D-LYSINE (DLYf)
11g: D-LYSINE (DLYg)
11h: D-LYSINE (DLYh)
11i: D-LYSINE (DLYi)
11j: D-LYSINE (DLYj)
12a: D-PHENYLALANINE (DPNa)
12b: D-PHENYLALANINE (DPNb)
12c: D-PHENYLALANINE (DPNc)
12d: D-PHENYLALANINE (DPNd)
12e: D-PHENYLALANINE (DPNe)
12f: D-PHENYLALANINE (DPNf)
12g: D-PHENYLALANINE (DPNg)
12h: D-PHENYLALANINE (DPNh)
13a: D-PROLINE (DPRa)
13b: D-PROLINE (DPRb)
13c: D-PROLINE (DPRc)
13d: D-PROLINE (DPRd)
13e: D-PROLINE (DPRe)
13f: D-PROLINE (DPRf)
14a: D-ASPARAGINE (DSGa)
14b: D-ASPARAGINE (DSGb)
14c: D-ASPARAGINE (DSGc)
14d: D-ASPARAGINE (DSGd)
15a: D-SERINE (DSNa)
15b: D-SERINE (DSNb)
15c: D-SERINE (DSNc)
15d: D-SERINE (DSNd)
15e: D-SERINE (DSNe)
15f: D-SERINE (DSNf)
15g: D-SERINE (DSNg)
15h: D-SERINE (DSNh)
15i: D-SERINE (DSNi)
15j: D-SERINE (DSNj)
15k: D-SERINE (DSNk)
15l: D-SERINE (DSNl)
15m: D-SERINE (DSNm)
15n: D-SERINE (DSNn)
16a: D-THREONINE (DTHa)
16b: D-THREONINE (DTHb)
16c: D-THREONINE (DTHc)
16d: D-THREONINE (DTHd)
17a: D-TRYPTOPHAN (DTRa)
17b: D-TRYPTOPHAN (DTRb)
18a: D-TYROSINE (DTYa)
18b: D-TYROSINE (DTYb)
19a: D-VALINE (DVAa)
19b: D-VALINE (DVAb)
19c: D-VALINE (DVAc)
19d: D-VALINE (DVAd)
19e: D-VALINE (DVAe)
19f: D-VALINE (DVAf)
20a: D-METHIONINE (MEDa)
20b: D-METHIONINE (MEDb)
20c: D-METHIONINE (MEDc)
20d: D-METHIONINE (MEDd)
21a: N-ACETYL-D-GLUCOSAMINE (NAGa)
21b: N-ACETYL-D-GLUCOSAMINE (NAGb)
22a: SULFATE ION (SO4a)
22aa: SULFATE ION (SO4aa)
22b: SULFATE ION (SO4b)
22c: SULFATE ION (SO4c)
22d: SULFATE ION (SO4d)
22e: SULFATE ION (SO4e)
22f: SULFATE ION (SO4f)
22g: SULFATE ION (SO4g)
22h: SULFATE ION (SO4h)
22i: SULFATE ION (SO4i)
22j: SULFATE ION (SO4j)
22k: SULFATE ION (SO4k)
22l: SULFATE ION (SO4l)
22m: SULFATE ION (SO4m)
22n: SULFATE ION (SO4n)
22o: SULFATE ION (SO4o)
22p: SULFATE ION (SO4p)
22q: SULFATE ION (SO4q)
22r: SULFATE ION (SO4r)
22s: SULFATE ION (SO4s)
22t: SULFATE ION (SO4t)
22u: SULFATE ION (SO4u)
22v: SULFATE ION (SO4v)
22w: SULFATE ION (SO4w)
22x: SULFATE ION (SO4x)
22y: SULFATE ION (SO4y)
22z: SULFATE ION (SO4z)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CIT
2
Ligand/Ion
CITRIC ACID
2
DAL
8
Mod. Amino Acid
D-ALANINE
3
DAR
16
Mod. Amino Acid
D-ARGININE
4
DAS
2
Mod. Amino Acid
D-ASPARTIC ACID
5
DCY
12
Mod. Amino Acid
D-CYSTEINE
6
DGL
8
Mod. Amino Acid
D-GLUTAMIC ACID
7
DGN
6
Mod. Amino Acid
D-GLUTAMINE
8
DHI
4
Mod. Amino Acid
D-HISTIDINE
9
DIL
8
Mod. Amino Acid
D-ISOLEUCINE
10
DLE
12
Mod. Amino Acid
D-LEUCINE
11
DLY
10
Mod. Amino Acid
D-LYSINE
12
DPN
8
Mod. Amino Acid
D-PHENYLALANINE
13
DPR
6
Mod. Amino Acid
D-PROLINE
14
DSG
4
Mod. Amino Acid
D-ASPARAGINE
15
DSN
14
Mod. Amino Acid
D-SERINE
16
DTH
4
Mod. Amino Acid
D-THREONINE
17
DTR
2
Mod. Amino Acid
D-TRYPTOPHAN
18
DTY
2
Mod. Amino Acid
D-TYROSINE
19
DVA
6
Mod. Amino Acid
D-VALINE
20
MED
4
Mod. Amino Acid
D-METHIONINE
21
NAG
-1
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
22
SO4
12
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(18, 18)
Info
All Sites
01: OC4 (SOFTWARE)
02: PC2 (SOFTWARE)
03: PC3 (SOFTWARE)
04: PC5 (SOFTWARE)
05: PC9 (SOFTWARE)
06: QC1 (SOFTWARE)
07: QC2 (SOFTWARE)
08: QC3 (SOFTWARE)
09: QC4 (SOFTWARE)
10: QC5 (SOFTWARE)
11: QC6 (SOFTWARE)
12: QC7 (SOFTWARE)
13: QC8 (SOFTWARE)
14: QC9 (SOFTWARE)
15: RC1 (SOFTWARE)
16: RC2 (SOFTWARE)
17: RC3 (SOFTWARE)
18: RC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
OC4
SOFTWARE
VAL A:56 , GLY A:57 , TRP A:58 , ARG A:61 , HOH A:210 , HOH A:219 , DSN D:36
BINDING SITE FOR RESIDUE SO4 A 103
02
PC2
SOFTWARE
DAR C:67 , DAR D:67
BINDING SITE FOR RESIDUE SO4 B 102
03
PC3
SOFTWARE
ARG B:10 , PRO B:70 , SER B:71 , LYS B:72 , HOH B:230 , DAR D:67
BINDING SITE FOR RESIDUE SO4 B 103
04
PC5
SOFTWARE
VAL B:56 , GLY B:57 , TRP B:58 , ARG B:61 , DSN C:36
BINDING SITE FOR RESIDUE SO4 B 105
05
PC9
SOFTWARE
ARG A:67 , ARG B:67 , DLY C:72
BINDING SITE FOR RESIDUE SO4 C 101
06
QC1
SOFTWARE
DSN C:32 , DSN C:33 , HOH C:216 , HOH C:223
BINDING SITE FOR RESIDUE SO4 C 102
07
QC2
SOFTWARE
ARG A:67 , DSN C:71 , DLY C:72 , HOH C:221
BINDING SITE FOR RESIDUE SO4 C 103
08
QC3
SOFTWARE
DGL C:19 , DAR C:23 , DAR C:61 , DHI C:62
BINDING SITE FOR RESIDUE SO4 C 104
09
QC4
SOFTWARE
DAR C:10 , DAR C:29 , DSG C:30
BINDING SITE FOR RESIDUE SO4 C 105
10
QC5
SOFTWARE
ARG A:10 , ARG A:29 , SER A:71 , LYS A:72 , DAR C:67
BINDING SITE FOR RESIDUE SO4 C 106
11
QC6
SOFTWARE
DAR C:67 , DHI C:68
BINDING SITE FOR RESIDUE SO4 C 107
12
QC7
SOFTWARE
SER B:33 , DVA C:56 , GLY C:57 , DTR C:58 , DAR C:61 , HOH C:214
BINDING SITE FOR RESIDUE CIT C 108
13
QC8
SOFTWARE
ARG B:67 , DSN D:71 , DLY D:72 , SO4 D:102
BINDING SITE FOR RESIDUE SO4 D 101
14
QC9
SOFTWARE
DPN C:8 , DAR D:29 , DGL D:49 , SO4 D:101 , HOH D:213
BINDING SITE FOR RESIDUE SO4 D 102
15
RC1
SOFTWARE
DAR D:10 , DAR D:29 , DSG D:30 , HOH D:217
BINDING SITE FOR RESIDUE SO4 D 103
16
RC2
SOFTWARE
DGL D:19 , DAR D:61 , DHI D:62
BINDING SITE FOR RESIDUE SO4 D 104
17
RC3
SOFTWARE
DAR D:67 , DHI D:68
BINDING SITE FOR RESIDUE SO4 D 105
18
RC4
SOFTWARE
SER A:33 , DGL D:19 , DVA D:56 , GLY D:57 , DTR D:58 , DAR D:61
BINDING SITE FOR RESIDUE CIT D 106
[
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 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 (124 KB)
Header - Asym.Unit
Biol.Unit 1 (59 KB)
Header - Biol.Unit 1
Biol.Unit 2 (56 KB)
Header - Biol.Unit 2
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
4OIK
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help