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2VNF
Asym. Unit
Info
Asym.Unit (53 KB)
Biol.Unit 1 (23 KB)
Biol.Unit 2 (26 KB)
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(1)
Title
:
MOLECULAR BASIS OF HISTONE H3K4ME3 RECOGNITION BY ING4
Authors
:
A. Palacios, I. G. Munoz, D. Pantoja-Uceda, M. J. Marcaida, D. Torres, J. M. Martin-Garcia, I. Luque, G. Montoya, F. J. Blanco
Date
:
04 Feb 08 (Deposition) - 01 Apr 08 (Release) - 28 Dec 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.76
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Acetylation, Alternative Splicing, Anti-Oncogene, Cell Cycle, Coiled C Nucleus, Zinc, Zinc-Finger, Ing4, Phd Finger, Histone 3
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Palacios, I. G. Munoz, D. Pantoja-Uceda, M. J. Marcaida, D. Torres, J. M. Martin-Garcia, I. Luque, G. Montoya, F. J. Blanco
Molecular Basis Of Histone H3K4Me3 Recognition By Ing4
J. Biol. Chem. V. 283 15956 2008
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Hetero Components
(5, 9)
Info
All Hetero Components
1a: 2,3-DIHYDROXY-1,4-DITHIOBUTANE (DTTa)
2a: (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-D... (DTUa)
3a: N-TRIMETHYLLYSINE (M3La)
3b: N-TRIMETHYLLYSINE (M3Lb)
4a: SODIUM ION (NAa)
5a: ZINC ION (ZNa)
5b: ZINC ION (ZNb)
5c: ZINC ION (ZNc)
5d: ZINC ION (ZNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DTT
1
Ligand/Ion
2,3-DIHYDROXY-1,4-DITHIOBUTANE
2
DTU
1
Ligand/Ion
(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
3
M3L
2
Mod. Amino Acid
N-TRIMETHYLLYSINE
4
NA
1
Ligand/Ion
SODIUM ION
5
ZN
4
Ligand/Ion
ZINC ION
[
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Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLN A:244 , DTT A:1245 , HOH A:2058 , HOH A:2059 , HOH A:2061
BINDING SITE FOR RESIDUE NA A 300
2
AC2
SOFTWARE
CYS A:199 , HIS A:202 , ILE A:219 , NA A:300 , HOH A:2007 , HOH A:2025 , HOH A:2048 , HOH A:2057 , HOH A:2060 , HOH A:2061
BINDING SITE FOR RESIDUE DTT A1245
3
AC3
SOFTWARE
HIS C:202 , ASN C:214 , GLN C:244 , HOH C:2031 , HOH C:2036 , HOH C:2039 , HOH C:2040 , HOH C:2041
BINDING SITE FOR RESIDUE DTU C1246
4
AC4
SOFTWARE
CYS A:199 , CYS A:201 , HIS A:223 , CYS A:226
BINDING SITE FOR RESIDUE ZN A1246
5
AC5
SOFTWARE
CYS C:199 , CYS C:201 , HIS C:223 , CYS C:226
BINDING SITE FOR RESIDUE ZN C1247
6
AC6
SOFTWARE
CYS C:212 , CYS C:217 , CYS C:239 , CYS C:242
BINDING SITE FOR RESIDUE ZN C1248
7
AC7
SOFTWARE
CYS A:212 , CYS A:217 , CYS A:239 , CYS A:242
BINDING SITE FOR RESIDUE ZN A1247
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: ZF_PHD_2 (A:196-244,C:196-244)
2: ZF_PHD_1 (A:199-242,C:199-242)
;
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.
ING4_HUMAN
196-245
2
A:196-244
C:196-244
2
ZF_PHD_1
PS01359
Zinc finger PHD-type signature.
ING4_HUMAN
199-242
2
A:199-242
C:199-242
[
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Exons
(3, 6)
Info
All Exons
Exon 1.10i (A:195-216 | C:191-216)
Exon 1.11b (A:217-237 | C:217-237)
Exon 1.11n (A:237-244 | C:237-244)
View:
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All Exon Boundaries
1: Boundary 1.10d/1.10i
2: Boundary 1.10i/1.11b
3: Boundary 1.11b/1.11n
4: Boundary 1.11n/-
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
1.1c
ENST00000396807
1c
ENSE00001945605
chr12:
6772306-6772231
76
ING4_HUMAN
1-13
13
0
-
-
1.7a
ENST00000396807
7a
ENSE00000866946
chr12:
6765964-6765893
72
ING4_HUMAN
13-37
25
0
-
-
1.9b
ENST00000396807
9b
ENSE00000715744
chr12:
6762562-6762396
167
ING4_HUMAN
37-92
56
0
-
-
1.10b
ENST00000396807
10b
ENSE00001789862
chr12:
6762216-6762102
115
ING4_HUMAN
93-131
39
0
-
-
1.10d
ENST00000396807
10d
ENSE00001526324
chr12:
6761936-6761828
109
ING4_HUMAN
131-167
37
0
-
-
1.10i
ENST00000396807
10i
ENSE00001721883
chr12:
6761584-6761437
148
ING4_HUMAN
167-216
50
2
A:195-216
C:191-216
22
26
1.11b
ENST00000396807
11b
ENSE00001640958
chr12:
6760551-6760490
62
ING4_HUMAN
217-237
21
2
A:217-237
C:217-237
21
21
1.11n
ENST00000396807
11n
ENSE00001876036
chr12:
6760400-6759757
644
ING4_HUMAN
237-249
13
2
A:237-244
C:237-244
8
8
[
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SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d2vnfa_ (A:)
1b: SCOP_d2vnfc_ (C:)
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Protein Domains
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Organisms
(
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(
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Class
:
Small proteins
(3458)
Fold
:
FYVE/PHD zinc finger
(57)
Superfamily
:
FYVE/PHD zinc finger
(57)
Family
:
PHD domain
(30)
Protein domain
:
automated matches
(12)
Human (Homo sapiens) [TaxId: 9606]
(5)
1a
d2vnfa_
A:
1b
d2vnfc_
C:
[
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
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Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_PHD_2vnfC01 (C:198-244)
1b: PFAM_PHD_2vnfC02 (C:198-244)
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Clan
:
zf-FYVE-PHD
(57)
Family
:
PHD
(44)
Homo sapiens (Human)
(33)
1a
PHD-2vnfC01
C:198-244
1b
PHD-2vnfC02
C:198-244
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Protein & NOT PROSITE
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Chain D
Asymmetric Unit 1
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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
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select residue range 5 to 10 in chain 'A'
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set fontsize 20
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show SS bonds with a radius of 100 units (=0.4Å)
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Asym.Unit (53 KB)
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