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.
3LQI
Asym. Unit
Info
Asym.Unit (104 KB)
Biol.Unit 1 (34 KB)
Biol.Unit 2 (35 KB)
Biol.Unit 3 (36 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 MLL1 PHD3-BROMO COMPLEXED WITH H3(1-9)K4ME2 PEPTIDE
Authors
:
Z. Wang, D. J. Patel
Date
:
09 Feb 10 (Deposition) - 07 Jul 10 (Release) - 28 Jul 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.92
Chains
:
Asym. Unit : A,B,C,R,S,T
Biol. Unit 1: A,R (1x)
Biol. Unit 2: B,S (1x)
Biol. Unit 3: C,T (1x)
Keywords
:
Phd Finger, Bromodomain, Mll1, Leukemia, H3(1-9)K4Me2, Chromosomal Protein, Dna-Binding, Nucleosome Core, Nucleus, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Z. Wang, J. Song, T. A. Milne, G. G. Wang, H. Li, C. D. Allis, D. J. Patel
Pro Isomerization In Mll1 Phd3-Bromo Cassette Connects H3K4Me Readout To Cyp33 And Hdac-Mediated Repression.
Cell(Cambridge, Mass. ) V. 141 1183 2010
[
close entry info
]
Hetero Components
(2, 9)
Info
All Hetero Components
1a: N-DIMETHYL-LYSINE (MLYa)
1b: N-DIMETHYL-LYSINE (MLYb)
1c: N-DIMETHYL-LYSINE (MLYc)
2a: ZINC ION (ZNa)
2b: ZINC ION (ZNb)
2c: ZINC ION (ZNc)
2d: ZINC ION (ZNd)
2e: ZINC ION (ZNe)
2f: ZINC ION (ZNf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MLY
3
Mod. Amino Acid
N-DIMETHYL-LYSINE
2
ZN
6
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
CYS A:1569 , CYS A:1572 , HIS A:1596 , CYS A:1599
BINDING SITE FOR RESIDUE ZN A 1
2
AC2
SOFTWARE
CYS A:1588 , CYS A:1591 , CYS A:1621 , CYS A:1624
BINDING SITE FOR RESIDUE ZN A 2
3
AC3
SOFTWARE
CYS B:1569 , CYS B:1572 , HIS B:1596 , CYS B:1599
BINDING SITE FOR RESIDUE ZN B 3
4
AC4
SOFTWARE
CYS B:1588 , CYS B:1591 , CYS B:1621 , CYS B:1624
BINDING SITE FOR RESIDUE ZN B 4
5
AC5
SOFTWARE
CYS C:1569 , CYS C:1572 , HIS C:1596 , CYS C:1599
BINDING SITE FOR RESIDUE ZN C 5
6
AC6
SOFTWARE
CYS C:1588 , CYS C:1591 , CYS C:1621 , CYS C:1624
BINDING SITE FOR RESIDUE ZN C 6
[
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
(2, 6)
Info
All PROSITE Patterns/Profiles
1: ZF_PHD_2 (-|-|A:1566-1627,B:1566-1627,C:1566...)
2: BROMODOMAIN_2 (A:1704-1748,B:1704-1748,C:1703-174...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ZF_PHD_2
PS50016
Zinc finger PHD-type profile.
KMT2A_HUMAN
1431-1482
1479-1533
1566-1627
3
-
-
A:1566-1627
B:1566-1627
C:1566-1627
2
BROMODOMAIN_2
PS50014
Bromodomain profile.
KMT2A_HUMAN
1703-1748
3
A:1704-1748
B:1704-1748
C:1703-1748
[
close PROSITE info
]
Exons
(1, 3)
Info
All Exons
Exon 1.2b (R:1-6 | S:1-7 | T:1-9)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.2b
2: Boundary 1.2b/-
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
1.2b
ENST00000359303
2b
ENSE00001974165
chr6:
27858570-27858160
411
H31_HUMAN
1-136
136
3
R:1-6
S:1-7
T:1-9
6
7
9
2.1a
ENST00000389506
1a
ENSE00002162629
chr11:
118307205-118307659
455
KMT2A_HUMAN
-
0
0
-
-
2.5b
ENST00000389506
5b
ENSE00001633768
chr11:
118339490-118339559
70
KMT2A_HUMAN
-
0
0
-
-
2.6a
ENST00000389506
6a
ENSE00001610993
chr11:
118342377-118345030
2654
KMT2A_HUMAN
1-298
298
0
-
-
2.7b
ENST00000389506
7b
ENSE00002192425
chr11:
118347520-118347697
178
KMT2A_HUMAN
299-358
60
0
-
-
2.8a
ENST00000389506
8a
ENSE00001785290
chr11:
118348682-118348916
235
KMT2A_HUMAN
358-436
79
0
-
-
2.9b
ENST00000389506
9b
ENSE00002148387
chr11:
118350889-118350953
65
KMT2A_HUMAN
436-451
16
0
-
-
2.10a
ENST00000389506
10a
ENSE00001660587
chr11:
118352430-118352807
378
KMT2A_HUMAN
-
0
0
-
-
2.11
ENST00000389506
11
ENSE00001619243
chr11:
118353137-118353210
74
KMT2A_HUMAN
-
0
0
-
-
2.12a
ENST00000389506
12a
ENSE00001735103
chr11:
118354898-118355029
132
KMT2A_HUMAN
-
0
0
-
-
2.13
ENST00000389506
13
ENSE00001703734
chr11:
118355577-118355690
114
KMT2A_HUMAN
-
0
0
-
-
2.15
ENST00000389506
15
ENSE00001775852
chr11:
118359329-118359475
147
KMT2A_HUMAN
-
0
0
-
-
2.16
ENST00000389506
16
ENSE00001798700
chr11:
118360507-118360602
96
KMT2A_HUMAN
-
0
0
-
-
2.17
ENST00000389506
17
ENSE00001621217
chr11:
118360844-118360964
121
KMT2A_HUMAN
-
0
0
-
-
2.18a
ENST00000389506
18a
ENSE00001785002
chr11:
118361911-118362024
114
KMT2A_HUMAN
-
0
0
-
-
2.19
ENST00000389506
19
ENSE00001611699
chr11:
118362459-118362643
185
KMT2A_HUMAN
-
0
0
-
-
2.20b
ENST00000389506
20b
ENSE00001749282
chr11:
118363772-118363945
174
KMT2A_HUMAN
-
0
0
-
-
2.21
ENST00000389506
21
ENSE00001625999
chr11:
118365003-118365113
111
KMT2A_HUMAN
-
0
0
-
-
2.22
ENST00000389506
22
ENSE00001642774
chr11:
118365409-118365482
74
KMT2A_HUMAN
-
0
0
-
-
2.23
ENST00000389506
23
ENSE00001729453
chr11:
118366415-118366608
194
KMT2A_HUMAN
-
0
0
-
-
2.24
ENST00000389506
24
ENSE00001671815
chr11:
118366976-118367082
107
KMT2A_HUMAN
-
0
0
-
-
2.25a
ENST00000389506
25a
ENSE00001513432
chr11:
118368651-118368723
73
KMT2A_HUMAN
-
0
0
-
-
[
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 R
Chain S
Chain T
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 (104 KB)
Header - Asym.Unit
Biol.Unit 1 (34 KB)
Header - Biol.Unit 1
Biol.Unit 2 (35 KB)
Header - Biol.Unit 2
Biol.Unit 3 (36 KB)
Header - Biol.Unit 3
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
3LQI
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help