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3LD8
Asym. Unit
Info
Asym.Unit (134 KB)
Biol.Unit 1 (128 KB)
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(1)
Title
:
STRUCTURE OF JMJD6 AND FAB FRAGMENTS
Authors
:
X. Hong, J. Zang, J. White, J. W. Kappler, C. Wang, G. Zhang
Date
:
12 Jan 10 (Deposition) - 04 Aug 10 (Release) - 20 Jun 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Jmjd6, Fab Fragments, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
X. Hong, J. Zang, J. White, C. Wang, C. H. Pan, R. Zhao, R. C. Murphy, S. Dai, P. Henson, J. W. Kappler, J. Hagman, G. Zhang
Interaction Of Jmjd6 With Single-Stranded Rna.
Proc. Natl. Acad. Sci. Usa V. 107 14568 2010
[
close entry info
]
Hetero Components
(4, 27)
Info
All Hetero Components
1a: FE (III) ION (FEa)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
3a: MERCURY (II) ION (HGa)
3b: MERCURY (II) ION (HGb)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
4e: SULFATE ION (SO4e)
4f: SULFATE ION (SO4f)
4g: SULFATE ION (SO4g)
4h: SULFATE ION (SO4h)
4i: SULFATE ION (SO4i)
4j: SULFATE ION (SO4j)
4k: SULFATE ION (SO4k)
4l: SULFATE ION (SO4l)
4m: SULFATE ION (SO4m)
4n: SULFATE ION (SO4n)
4o: SULFATE ION (SO4o)
4p: SULFATE ION (SO4p)
4q: SULFATE ION (SO4q)
4r: SULFATE ION (SO4r)
4s: SULFATE ION (SO4s)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FE
1
Ligand/Ion
FE (III) ION
2
GOL
5
Ligand/Ion
GLYCEROL
3
HG
2
Ligand/Ion
MERCURY (II) ION
4
SO4
19
Ligand/Ion
SULFATE ION
[
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Sites
(26, 26)
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)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TRP A:206 , CYS A:207
BINDING SITE FOR RESIDUE HG A 335
02
AC2
SOFTWARE
CYS A:101 , MET A:112
BINDING SITE FOR RESIDUE HG A 336
03
AC3
SOFTWARE
ASP A:50 , GLN A:53 , GLU A:58 , ARG A:62 , SER C:54
BINDING SITE FOR RESIDUE GOL A 337
04
AC4
SOFTWARE
ASP A:279 , THR A:280
BINDING SITE FOR RESIDUE GOL A 338
05
AC5
SOFTWARE
MET A:1 , SER A:5 , LYS A:6 , GLU A:119 , SER A:123
BINDING SITE FOR RESIDUE GOL A 339
06
AC6
SOFTWARE
ARG A:95 , ASN A:96 , LYS A:115
BINDING SITE FOR RESIDUE GOL A 340
07
AC7
SOFTWARE
GLU A:334 , ARG B:114
BINDING SITE FOR RESIDUE GOL B 221
08
AC8
SOFTWARE
ASN A:237 , ASN C:53 , TYR C:100
BINDING SITE FOR RESIDUE SO4 A 341
09
AC9
SOFTWARE
ARG C:71
BINDING SITE FOR RESIDUE SO4 C 222
10
BC1
SOFTWARE
ASN A:96 , GLN A:97
BINDING SITE FOR RESIDUE SO4 A 342
11
BC2
SOFTWARE
SER A:109 , LYS A:111 , SER A:136
BINDING SITE FOR RESIDUE SO4 A 343
12
BC3
SOFTWARE
LEU A:147 , ARG A:173
BINDING SITE FOR RESIDUE SO4 A 344
13
BC4
SOFTWARE
THR A:221 , ARG A:222 , GLN A:229
BINDING SITE FOR RESIDUE SO4 A 345
14
BC5
SOFTWARE
GLN B:48 , SER B:49 , LYS B:51 , GLN C:110
BINDING SITE FOR RESIDUE SO4 B 222
15
BC6
SOFTWARE
ARG A:8 , LYS A:113 , TYR A:116
BINDING SITE FOR RESIDUE SO4 A 346
16
BC7
SOFTWARE
GLY A:165 , GLU A:166 , LYS A:167 , ARG A:168
BINDING SITE FOR RESIDUE SO4 A 347
17
BC8
SOFTWARE
LEU A:191 , LYS A:300
BINDING SITE FOR RESIDUE SO4 A 348
18
BC9
SOFTWARE
ARG A:215 , GLU A:216
BINDING SITE FOR RESIDUE SO4 A 349
19
CC1
SOFTWARE
LYS A:307 , ARG A:310 , ARG A:314
BINDING SITE FOR RESIDUE SO4 A 350
20
CC2
SOFTWARE
ARG A:305 , PRO A:306 , LYS A:307 , LEU A:308
BINDING SITE FOR RESIDUE SO4 A 351
21
CC3
SOFTWARE
LYS B:18 , THR B:20 , SER B:71 , GLY B:72 , ASP B:76 , THR B:78 , THR B:80
BINDING SITE FOR RESIDUE SO4 B 223
22
CC4
SOFTWARE
SER B:182 , THR B:184 , PHE C:173 , PRO C:174 , VAL C:176 , SER C:183 , LEU C:184 , SER C:185
BINDING SITE FOR RESIDUE SO4 C 223
23
CC5
SOFTWARE
HIS A:187 , ASP A:189 , HIS A:273
BINDING SITE FOR RESIDUE FE A 601
24
CC6
SOFTWARE
ASP A:328
BINDING SITE FOR RESIDUE SO4 A 352
25
CC7
SOFTWARE
LYS A:84 , ARG A:89 , LYS A:93
BINDING SITE FOR RESIDUE SO4 A 353
26
CC8
SOFTWARE
ARG A:95
BINDING SITE FOR RESIDUE SO4 A 354
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: JMJC (A:141-305)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
JMJC
PS51184
JmjC domain profile.
JMJD6_HUMAN
141-305
1
A:141-305
[
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Exons
(0, 0)
Info
All Exons
View:
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Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d3ld8b1 (B:1-113)
1b: SCOP_d3ld8b2 (B:114-217)
View:
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Classes
(
)
(
)
Folds
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Superfamilies
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)
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)
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Immunoglobulin
(5995)
Family
:
automated matches
(864)
Protein domain
:
automated matches
(864)
Cricetulus migratorius [TaxId: 10032]
(5)
1a
d3ld8b1
B:1-113
1b
d3ld8b2
B:114-217
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_JmjC_3ld8A01 (A:174-288)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Cupin
(179)
Family
:
JmjC
(39)
Homo sapiens (Human)
(31)
1a
JmjC-3ld8A01
A:174-288
[
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]
Atom Selection
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Nucleic
Backbone
Sidechain
Hetero
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Solvent
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Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Asymmetric Unit 1
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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)
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Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
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Asym.Unit (134 KB)
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