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.
3ZMV
Asym. Unit
Info
Asym.Unit (142 KB)
Biol.Unit 1 (133 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
LSD1-COREST IN COMPLEX WITH PLSFLV PEPTIDE
Authors
:
M. Tortorici, M. T. Borrello, M. Tardugno, L. R. Chiarelli, S. Pilotto, G. Ciossani, N. A. Vellore, J. Cowan, M. O'Connell, A. Mai, R. Baron, A. A. Mattevi
Date
:
12 Feb 13 (Deposition) - 12 Jun 13 (Release) - 28 Aug 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Transcription, Transcription Factor, Chromatin
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Tortorici, M. T. Borrello, M. Tardugno, L. R. Chiarelli, S. Pilotto G. Ciossani, N. A. Vellore, S. G. Bailey, J. Cowan, M. O'Connell, S. J. Crabb, G. K. Packham, A. Mai, R. Baron, A. Ganesan, A. Mattevi
Protein Recognition By Small Peptide Reversible Inhibitors Of The Chromatin-Modifying Lsd1/Corest Lysine Demethylase.
Acs Chem. Biol. V. 8 1677 2013
[
close entry info
]
Hetero Components
(1, 1)
Info
All Hetero Components
1a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FAD
1
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
[
close Hetero Component info
]
Sites
(1, 1)
Info
All Sites
1: AC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLY A:285 , GLY A:287 , VAL A:288 , SER A:289 , LEU A:307 , GLU A:308 , ALA A:309 , ARG A:310 , GLY A:314 , GLY A:315 , ARG A:316 , VAL A:317 , LEU A:329 , GLY A:330 , ALA A:331 , MET A:332 , VAL A:333 , THR A:588 , VAL A:590 , THR A:624 , LEU A:625 , PRO A:626 , VAL A:637 , TRP A:756 , SER A:760 , TYR A:761 , GLY A:800 , GLU A:801 , ALA A:809 , THR A:810 , VAL A:811 , ALA A:814 , PHE C:4
BINDING SITE FOR RESIDUE FAD A 900
[
close Site info
]
SAPs(SNPs)/Variants
(3, 3)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_076366 (E379K, chain A, )
2: VAR_076367 (D556G, chain A, )
3: VAR_076368 (Y761H, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_076366
E
379
K
KDM1A_HUMAN
Disease (CPRF)
864309715
A
E
379
K
2
UniProt
VAR_076367
D
556
G
KDM1A_HUMAN
Disease (CPRF)
864309716
A
D
556
G
3
UniProt
VAR_076368
Y
761
H
KDM1A_HUMAN
Disease (CPRF)
864309714
A
Y
761
H
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: SWIRM (A:174-273)
2: SANT (-|B:378-429)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
SWIRM
PS50934
SWIRM domain profile.
KDM1A_HUMAN
174-273
1
A:174-273
2
SANT
PS51293
SANT domain profile.
RCOR1_HUMAN
190-241
381-432
1
-
B:378-429
[
close PROSITE info
]
Exons
(22, 22)
Info
All Exons
Exon 1.8 (B:308-345)
Exon 1.9 (B:346-371)
Exon 1.10 (B:372-391)
Exon 1.11 (B:391-440)
Exon 2.2 (A:172-173)
Exon 2.4a (A:173-217)
Exon 2.5 (A:218-244)
Exon 2.6a (A:244-275)
Exon 2.7 (A:275-310)
Exon 2.8 (A:311-338)
Exon 2.9 (A:338-369)
Exon 2.11 (A:370-417)
Exon 2.12 (A:417-447)
Exon 2.13 (A:448-492)
Exon 2.14 (A:493-517)
Exon 2.15b (A:517-554)
Exon 2.16a (A:555-599)
Exon 2.17b (A:599-661)
Exon 2.18b (A:662-700)
Exon 2.19 (A:700-742)
Exon 2.20 (A:743-791)
Exon 2.21c (A:792-836)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.7/1.8
02: Boundary 1.8/1.9
03: Boundary 1.9/1.10
04: Boundary 1.10/1.11
05: Boundary 1.11/1.12
06: Boundary 2.1a/2.2
07: Boundary 2.2/2.4a
08: Boundary 2.4a/2.5
09: Boundary 2.5/2.6a
10: Boundary 2.6a/2.7
11: Boundary 2.7/2.8
12: Boundary 2.8/2.9
13: Boundary 2.9/2.11
14: Boundary 2.11/2.12
15: Boundary 2.12/2.13
16: Boundary 2.13/2.14
17: Boundary 2.14/2.15b
18: Boundary 2.15b/2.16a
19: Boundary 2.16a/2.17b
20: Boundary 2.17b/2.18b
21: Boundary 2.18b/2.19
22: Boundary 2.19/2.20
23: Boundary 2.20/2.21c
24: Boundary 2.21c/-
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
1.1
ENST00000262241
1
ENSE00001420913
chr14:
103059233-103059524
292
RCOR1_HUMAN
1-98
98
0
-
-
1.2
ENST00000262241
2
ENSE00000660501
chr14:
103059603-103059662
60
RCOR1_HUMAN
98-118
21
0
-
-
1.3
ENST00000262241
3
ENSE00000870514
chr14:
103148232-103148315
84
RCOR1_HUMAN
118-146
29
0
-
-
1.4
ENST00000262241
4
ENSE00001678988
chr14:
103167615-103167667
53
RCOR1_HUMAN
146-163
18
0
-
-
1.5
ENST00000262241
5
ENSE00001719953
chr14:
103173688-103173849
162
RCOR1_HUMAN
164-217
54
0
-
-
1.6
ENST00000262241
6
ENSE00000660506
chr14:
103174802-103174920
119
RCOR1_HUMAN
218-257
40
0
-
-
1.7
ENST00000262241
7
ENSE00000870515
chr14:
103177272-103177350
79
RCOR1_HUMAN
257-283
27
0
-
-
1.8
ENST00000262241
8
ENSE00000660508
chr14:
103180760-103180954
195
RCOR1_HUMAN
284-348
65
1
B:308-345
38
1.9
ENST00000262241
9
ENSE00000660509
chr14:
103187344-103187421
78
RCOR1_HUMAN
349-374
26
1
B:346-371
26
1.10
ENST00000262241
10
ENSE00000660510
chr14:
103187657-103187714
58
RCOR1_HUMAN
375-394
20
1
B:372-391
20
1.11
ENST00000262241
11
ENSE00000870516
chr14:
103188524-103188753
230
RCOR1_HUMAN
394-470
77
1
B:391-440
50
1.12
ENST00000262241
12
ENSE00001152549
chr14:
103192805-103196912
4108
RCOR1_HUMAN
471-482
12
0
-
-
2.1a
ENST00000356634
1a
ENSE00001422377
chr1:
23345941-23346440
500
KDM1A_HUMAN
1-117
117
0
-
-
2.2
ENST00000356634
2
ENSE00000388542
chr1:
23356962-23357127
166
KDM1A_HUMAN
118-173
56
1
A:172-173
2
2.4a
ENST00000356634
4a
ENSE00000759117
chr1:
23376880-23377013
134
KDM1A_HUMAN
173-217
45
1
A:173-217
45
2.5
ENST00000356634
5
ENSE00000859702
chr1:
23380254-23380332
79
KDM1A_HUMAN
218-244
27
1
A:218-244
27
2.6a
ENST00000356634
6a
ENSE00000859703
chr1:
23381562-23381654
93
KDM1A_HUMAN
244-275
32
1
A:244-275
32
2.7
ENST00000356634
7
ENSE00000859704
chr1:
23382425-23382531
107
KDM1A_HUMAN
275-310
36
1
A:275-310
36
2.8
ENST00000356634
8
ENSE00000859705
chr1:
23383977-23384058
82
KDM1A_HUMAN
311-338
28
1
A:311-338
28
2.9
ENST00000356634
9
ENSE00000759111
chr1:
23385566-23385660
95
KDM1A_HUMAN
338-369
32
1
A:338-369
32
2.11
ENST00000356634
11
ENSE00000759110
chr1:
23395032-23395174
143
KDM1A_HUMAN
370-417
48
1
A:370-417
48
2.12
ENST00000356634
12
ENSE00000759108
chr1:
23395554-23395644
91
KDM1A_HUMAN
417-447
31
1
A:417-447
31
2.13
ENST00000356634
13
ENSE00000859709
chr1:
23397718-23397852
135
KDM1A_HUMAN
448-492
45
1
A:448-492
45
2.14
ENST00000356634
14
ENSE00000759106
chr1:
23398617-23398690
74
KDM1A_HUMAN
493-517
25
1
A:493-517
25
2.15b
ENST00000356634
15b
ENSE00000388553
chr1:
23399785-23399896
112
KDM1A_HUMAN
517-554
38
1
A:517-554
38
2.16a
ENST00000356634
16a
ENSE00000759050
chr1:
23403721-23403853
133
KDM1A_HUMAN
555-599
45
1
A:555-599
45
2.17b
ENST00000356634
17b
ENSE00000859713
chr1:
23405483-23405670
188
KDM1A_HUMAN
599-661
63
1
A:599-661
63
2.18b
ENST00000356634
18b
ENSE00000859714
chr1:
23406046-23406160
115
KDM1A_HUMAN
662-700
39
1
A:662-700
39
2.19
ENST00000356634
19
ENSE00000859715
chr1:
23407939-23408066
128
KDM1A_HUMAN
700-742
43
1
A:700-742
43
2.20
ENST00000356634
20
ENSE00000759046
chr1:
23408713-23408859
147
KDM1A_HUMAN
743-791
49
1
A:743-791
49
2.21c
ENST00000356634
21c
ENSE00001564450
chr1:
23409672-23410182
511
KDM1A_HUMAN
792-852
61
1
A:792-836
45
[
close EXON info
]
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 (142 KB)
Header - Asym.Unit
Biol.Unit 1 (133 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
3ZMV
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
