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3KV4
Biol. Unit 1
Info
Asym.Unit (86 KB)
Biol.Unit 1 (80 KB)
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(1)
Title
:
STRUCTURE OF PHF8 IN COMPLEX WITH HISTONE H3
Authors
:
J. R. Horton, A. K. Upadhyay, H. H. Qi, X. Zhang, Y. Shi, X. Cheng
Date
:
29 Nov 09 (Deposition) - 22 Dec 09 (Release) - 09 Feb 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.19
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Epigenetics, Histone Code, Covalent Histone Modifications, Jumonji Demethylase, Mental Retardation, Metal-Binding, Zinc, Zinc-Finger
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. R. Horton, A. K. Upadhyay, H. H. Qi, X. Zhang, Y. Shi, X. Cheng
Enzymatic And Structural Insights For Substrate Specificity Of A Family Of Jumonji Histone Lysine Demethylases.
Nat. Struct. Mol. Biol. V. 17 38 2010
[
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Hetero Components
(5, 17)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1b: 1,2-ETHANEDIOL (EDOb)
1c: 1,2-ETHANEDIOL (EDOc)
1d: 1,2-ETHANEDIOL (EDOd)
1e: 1,2-ETHANEDIOL (EDOe)
1f: 1,2-ETHANEDIOL (EDOf)
1g: 1,2-ETHANEDIOL (EDOg)
1h: 1,2-ETHANEDIOL (EDOh)
1i: 1,2-ETHANEDIOL (EDOi)
1j: 1,2-ETHANEDIOL (EDOj)
1k: 1,2-ETHANEDIOL (EDOk)
1l: 1,2-ETHANEDIOL (EDOl)
1m: 1,2-ETHANEDIOL (EDOm)
2a: FE (II) ION (FE2a)
3a: N-TRIMETHYLLYSINE (M3La)
4a: N-DIMETHYL-LYSINE (MLYa)
5a: NICKEL (II) ION (NIa)
6a: N-OXALYLGLYCINE (OGAa)
7a: ZINC ION (ZNa)
7b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
13
Ligand/Ion
1,2-ETHANEDIOL
2
FE2
1
Ligand/Ion
FE (II) ION
3
M3L
1
Mod. Amino Acid
N-TRIMETHYLLYSINE
4
MLY
1
Mod. Amino Acid
N-DIMETHYL-LYSINE
5
NI
-1
Ligand/Ion
NICKEL (II) ION
6
OGA
1
Ligand/Ion
N-OXALYLGLYCINE
7
ZN
-1
Ligand/Ion
ZINC ION
[
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Sites
(18, 18)
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)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
CYS A:8 , CYS A:10 , HIS A:31 , CYS A:34 , EDO A:452
BINDING SITE FOR RESIDUE ZN A 448
02
AC2
SOFTWARE
CYS A:23 , CYS A:26 , CYS A:50 , CYS A:53
BINDING SITE FOR RESIDUE ZN A 449
03
AC3
SOFTWARE
HIS A:247 , ASP A:249 , HIS A:319 , HOH A:553 , OGA A:5798
BINDING SITE FOR RESIDUE FE2 A 450
04
AC4
SOFTWARE
SER A:214 , TRP A:215 , VAL A:216 , PHE A:334 , LEU A:335
BINDING SITE FOR RESIDUE NI A 451
05
AC5
SOFTWARE
CYS A:10 , LEU A:12 , ARG A:18 , HIS A:31 , CYS A:34 , LEU A:104 , PHE A:115 , GLU A:118 , ASN A:119 , ZN A:448 , HOH A:472
BINDING SITE FOR RESIDUE EDO A 452
06
AC6
SOFTWARE
ARG A:92 , ASN A:202 , ILE A:265 , LYS A:302
BINDING SITE FOR RESIDUE EDO A 453
07
AC7
SOFTWARE
PHE A:96 , SER A:98 , ARG A:199 , HOH A:500 , HOH A:512 , HOH A:608
BINDING SITE FOR RESIDUE EDO A 454
08
AC8
SOFTWARE
ARG A:270 , HOH A:514
BINDING SITE FOR RESIDUE EDO A 455
09
AC9
SOFTWARE
ARG A:18 , SER A:33 , GLU A:118
BINDING SITE FOR RESIDUE EDO A 456
10
BC1
SOFTWARE
LYS A:212 , LEU A:213 , SER A:214 , TRP A:215 , EDO A:459
BINDING SITE FOR RESIDUE EDO A 457
11
BC2
SOFTWARE
ARG A:89 , ASP A:131 , GLY A:132 , GLY A:134
BINDING SITE FOR RESIDUE EDO A 458
12
BC3
SOFTWARE
SER A:337 , HIS A:374 , ILE A:378 , EDO A:457
BINDING SITE FOR RESIDUE EDO A 459
13
BC4
SOFTWARE
ASP A:44 , ILE A:45 , SER A:60 , ILE A:61 , MET A:62
BINDING SITE FOR RESIDUE EDO A 460
14
BC5
SOFTWARE
VAL A:35 , VAL A:37 , TYR A:48 , HIS A:49 , PRO A:51 , GLU A:54
BINDING SITE FOR RESIDUE EDO A 461
15
BC6
SOFTWARE
ASN A:52 , VAL A:55 , SER A:98 , ASP A:100 , GLU A:101
BINDING SITE FOR RESIDUE EDO A 462
16
BC7
SOFTWARE
THR A:355
BINDING SITE FOR RESIDUE EDO A 463
17
BC8
SOFTWARE
ASP A:161 , CYS A:168 , MET A:170 , LYS A:186
BINDING SITE FOR RESIDUE EDO A 464
18
BC9
SOFTWARE
ASN A:189 , THR A:244 , HIS A:247 , ASP A:249 , TYR A:257 , LYS A:264 , HIS A:319 , VAL A:321 , FE2 A:450 , HOH A:479 , HOH A:553 , MLY B:9
BINDING SITE FOR RESIDUE OGA A 5798
[
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]
SAPs(SNPs)/Variants
(1, 1)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_062250 (F279S, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_062250
F
315
S
PHF8_HUMAN
Disease (MRXSSD)
---
A
F
279
S
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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PROSITE Patterns/Profiles
(4, 4)
Info
All PROSITE Patterns/Profiles
1: HISTONE_H3_1 (B:14-14)
2: ZF_PHD_2 (A:5-56)
3: ZF_PHD_1 (A:8-53)
4: JMJC (A:195-351)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
HISTONE_H3_1
PS00322
Histone H3 signature 1.
H3C_HUMAN
15-21
1
B:14-14
2
ZF_PHD_2
PS50016
Zinc finger PHD-type profile.
PHF8_HUMAN
41-92
1
A:5-56
3
ZF_PHD_1
PS01359
Zinc finger PHD-type signature.
PHF8_HUMAN
44-89
1
A:8-53
4
JMJC
PS51184
JmjC domain profile.
PHF8_HUMAN
231-387
1
A:195-351
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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:
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Label:
Sorry, no Info available
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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
(2, 2)
Info
all PFAM domains
1a: PFAM_JmjC_3kv4A01 (A:234-334)
2a: PFAM_PHD_3kv4A02 (A:7-56)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Cupin
(179)
Family
:
JmjC
(39)
Homo sapiens (Human)
(31)
1a
JmjC-3kv4A01
A:234-334
Clan
:
zf-FYVE-PHD
(57)
Family
:
PHD
(44)
Homo sapiens (Human)
(33)
2a
PHD-3kv4A02
A:7-56
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Asymmetric Unit 1
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select chains 'A' and 'C'
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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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select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
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wireframe 100
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