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.
3CE4
Asym. Unit
Info
Asym.Unit (70 KB)
Biol.Unit 1 (64 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF MACROPHAGE MIGRATION INHIBITORY FACTOR COVALENTLY INHIBITED BY PMSF TREATMENT
Authors
:
G. V. Crichlow, E. Lolis
Date
:
28 Feb 08 (Deposition) - 30 Dec 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.55
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Covalent Modification, Covalent Inhibition, Cytokine, Inflammatory Response, Isomerase, Phosphoprotein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. V. Crichlow, J. B. Lubetsky, L. Leng, R. Bucala, E. J. Lolis
Structural And Kinetic Analyses Of Macrophage Migration Inhibitory Factor Active Site Interactions.
Biochemistry V. 48 132 2009
[
close entry info
]
Hetero Components
(4, 13)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
2a: ISOPROPYL ALCOHOL (IPAa)
2b: ISOPROPYL ALCOHOL (IPAb)
3a: PHENYLMETHANESULFONIC ACID (PMSa)
3b: PHENYLMETHANESULFONIC ACID (PMSb)
3c: PHENYLMETHANESULFONIC ACID (PMSc)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
4e: SULFATE ION (SO4e)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
3
Ligand/Ion
GLYCEROL
2
IPA
2
Ligand/Ion
ISOPROPYL ALCOHOL
3
PMS
3
Ligand/Ion
PHENYLMETHANESULFONIC ACID
4
SO4
5
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(13, 13)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLY A:68 , GLY A:69 , ALA A:70 , GLN A:71 , HOH A:482 , HOH A:548 , HOH A:635
BINDING SITE FOR RESIDUE SO4 A 901
02
AC2
SOFTWARE
ALA A:70 , ARG A:73 , HOH A:243
BINDING SITE FOR RESIDUE SO4 A 904
03
AC3
SOFTWARE
GLY B:68 , GLY B:69 , ALA B:70 , GLN B:71 , HOH B:554
BINDING SITE FOR RESIDUE SO4 B 902
04
AC4
SOFTWARE
GLY C:68 , GLY C:69 , ALA C:70 , GLN C:71 , HOH C:456 , HOH C:575 , HOH C:644
BINDING SITE FOR RESIDUE SO4 C 903
05
AC5
SOFTWARE
ARG C:73 , HOH C:255
BINDING SITE FOR RESIDUE SO4 C 905
06
AC6
SOFTWARE
PRO A:1 , MET A:2 , LYS A:32 , HIS A:62 , SER A:63 , ILE A:64 , VAL A:106 , GLN C:24 , TYR C:95 , ASN C:97
BINDING SITE FOR RESIDUE PMS A 200
07
AC7
SOFTWARE
GLN A:24 , TYR A:95 , ASN A:97 , PRO B:1 , MET B:2 , LYS B:32 , HIS B:62 , SER B:63 , ILE B:64
BINDING SITE FOR RESIDUE PMS B 200
08
AC8
SOFTWARE
TYR B:95 , ASN B:97 , PRO C:1 , MET C:2 , LYS C:32 , HIS C:62 , SER C:63 , ILE C:64 , VAL C:106
BINDING SITE FOR RESIDUE PMS C 200
09
AC9
SOFTWARE
GLU A:85 , ARG A:86 , HOH A:619 , GLY B:65 , LYS B:66 , HOH B:506
BINDING SITE FOR RESIDUE GOL B 702
10
BC1
SOFTWARE
ASN A:109 , GLY B:50 , SER B:52 , HOH B:579 , ASP C:92 , HOH C:264
BINDING SITE FOR RESIDUE GOL B 703
11
BC2
SOFTWARE
HOH A:230 , HOH A:310 , GLN B:35 , TRP B:108
BINDING SITE FOR RESIDUE IPA B 801
12
BC3
SOFTWARE
SER B:20 , GLY C:65 , LYS C:66 , GLN C:71 , HOH C:267 , HOH C:644 , HOH C:650
BINDING SITE FOR RESIDUE GOL C 701
13
BC4
SOFTWARE
PRO C:15 , ASP C:16
BINDING SITE FOR RESIDUE IPA C 802
[
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
(1, 3)
Info
All PROSITE Patterns/Profiles
1: MIF (A:54-68,B:54-68,C:54-68)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
MIF
PS01158
Macrophage migration inhibitory factor family signature.
MIF_HUMAN
55-69
3
A:54-68
B:54-68
C:54-68
[
close PROSITE info
]
Exons
(3, 9)
Info
All Exons
Exon 1.1a (A:1-35 | B:1-35 | C:1-35)
Exon 1.2b (A:36-93 | B:36-93 | C:36-93)
Exon 1.2d (A:93-114 | B:93-114 | C:93-114)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.1a
2: Boundary 1.1a/1.2b
3: Boundary 1.2b/1.2d
4: Boundary 1.2d/-
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
ENST00000215754
1a
ENSE00001922200
chr22:
24236191-24236769
579
MIF_HUMAN
1-36
36
3
A:1-35
B:1-35
C:1-35
35
35
35
1.2b
ENST00000215754
2b
ENSE00000651496
chr22:
24236959-24237131
173
MIF_HUMAN
37-94
58
3
A:36-93
B:36-93
C:36-93
58
58
58
1.2d
ENST00000215754
2d
ENSE00001839840
chr22:
24237227-24237413
187
MIF_HUMAN
94-115
22
3
A:93-114
B:93-114
C:93-114
22
22
22
[
close EXON info
]
SCOP Domains
(1, 3)
Info
All SCOP Domains
1a: SCOP_d3ce4a_ (A:)
1b: SCOP_d3ce4b_ (B:)
1c: SCOP_d3ce4c_ (C:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Tautomerase/MIF
(104)
Superfamily
:
Tautomerase/MIF
(104)
Family
:
MIF-related
(58)
Protein domain
:
Microphage migration inhibition factor (MIF)
(55)
Human (Homo sapiens) [TaxId: 9606]
(46)
1a
d3ce4a_
A:
1b
d3ce4b_
B:
1c
d3ce4c_
C:
[
close SCOP info
]
CATH Domains
(1, 3)
Info
all CATH domains
1a: CATH_3ce4A00 (A:1-114)
1b: CATH_3ce4C00 (C:1-114)
1c: CATH_3ce4B00 (B:1-114)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Macrophage Migration Inhibitory Factor
(40)
Homologous Superfamily
:
Macrophage Migration Inhibitory Factor
(40)
Human (Homo sapiens)
(25)
1a
3ce4A00
A:1-114
1b
3ce4C00
C:1-114
1c
3ce4B00
B:1-114
[
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
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 (70 KB)
Header - Asym.Unit
Biol.Unit 1 (64 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
3CE4
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help