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Getting 'Exon' information from database.
4DGI
Asym. Unit
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Asym.Unit (94 KB)
Biol.Unit 1 (89 KB)
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(1)
Title
:
STRUCTURE OF POM1 FAB FRAGMENT COMPLEXED WITH HUMAN PRPC FRAGMENT 120-230
Authors
:
P. K. Baral, B. Wieland, M. Swayampakula, M. N. James
Date
:
26 Jan 12 (Deposition) - 31 Oct 12 (Release) - 23 Jan 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,H,L
Biol. Unit 1: A,H,L (1x)
Keywords
:
Prion, Antibody, Protein Binding
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. K. Baral, B. Wieland, M. Swayampakula, M. Polymenidou, M. H. Rahman N. N. Kav, A. Aguzzi, M. N. James
Structural Studies On The Folded Domain Of The Human Prion Protein Bound To The Fab Fragment Of The Antibody Pom1.
Acta Crystallogr. , Sect. D V. 68 1501 2012
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 1)
Info
All Hetero Components
1a: SODIUM ION (NAa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NA
1
Ligand/Ion
SODIUM ION
[
close Hetero Component info
]
Sites
(1, 1)
Info
All Sites
1: AC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
SER H:191 , SER H:195 , GLU H:196 , GLU L:79 , GLU L:81
BINDING SITE FOR RESIDUE NA L 300
[
close Site info
]
SAPs(SNPs)/Variants
(20, 20)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_006467 (M129V, chain A, )
02: VAR_014264 (G131V, chain A, )
03: VAR_006468 (N171S, chain A, )
04: VAR_006469 (D178N, chain A, )
05: VAR_006470 (V180I, chain A, )
06: VAR_006471 (T183A, chain A, )
07: VAR_008746 (H187R, chain A, )
08: VAR_008748 (T188K, chain A, )
09: VAR_008747 (T188R, chain A, )
10: VAR_008749 (E196K, chain A, )
11: VAR_006472 (F198S, chain A, )
12: VAR_006473 (E200K, chain A, )
13: VAR_008750 (D202N, chain A, )
14: VAR_008751 (V203I, chain A, )
15: VAR_006474 (R208H, chain A, )
16: VAR_006475 (V210I, chain A, )
17: VAR_008752 (E211Q, chain A, )
18: VAR_008753 (Q212P, chain A, )
19: VAR_006476 (Q217R, chain A, )
20: VAR_006477 (E219K, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_006467
M
129
V
PRIO_HUMAN
Polymorphism
1799990
A
M
129
V
02
UniProt
VAR_014264
G
131
V
PRIO_HUMAN
Disease (GSD)
---
A
G
131
V
03
UniProt
VAR_006468
N
171
S
PRIO_HUMAN
Polymorphism
16990018
A
N
171
S
04
UniProt
VAR_006469
D
178
N
PRIO_HUMAN
Disease (FFI)
---
A
D
178
N
05
UniProt
VAR_006470
V
180
I
PRIO_HUMAN
Disease (CJD)
---
A
V
180
I
06
UniProt
VAR_006471
T
183
A
PRIO_HUMAN
Unclassified
---
A
T
183
A
07
UniProt
VAR_008746
H
187
R
PRIO_HUMAN
Disease (GSD)
---
A
H
187
R
08
UniProt
VAR_008748
T
188
K
PRIO_HUMAN
Unclassified
---
A
T
188
K
09
UniProt
VAR_008747
T
188
R
PRIO_HUMAN
Polymorphism
---
A
T
188
R
10
UniProt
VAR_008749
E
196
K
PRIO_HUMAN
Disease (CJD)
---
A
E
196
K
11
UniProt
VAR_006472
F
198
S
PRIO_HUMAN
Disease (GSD)
---
A
F
198
S
12
UniProt
VAR_006473
E
200
K
PRIO_HUMAN
Disease (CJD)
---
A
E
200
K
13
UniProt
VAR_008750
D
202
N
PRIO_HUMAN
Disease (GSD)
---
A
D
202
N
14
UniProt
VAR_008751
V
203
I
PRIO_HUMAN
Disease (CJD)
---
A
V
203
I
15
UniProt
VAR_006474
R
208
H
PRIO_HUMAN
Disease (CJD)
---
A
R
208
H
16
UniProt
VAR_006475
V
210
I
PRIO_HUMAN
Disease (CJD)
---
A
V
210
I
17
UniProt
VAR_008752
E
211
Q
PRIO_HUMAN
Disease (CJD)
---
A
E
211
Q
18
UniProt
VAR_008753
Q
212
P
PRIO_HUMAN
Disease (GSD)
---
A
Q
212
P
19
UniProt
VAR_006476
Q
217
R
PRIO_HUMAN
Disease (GSD)
---
A
Q
217
R
20
UniProt
VAR_006477
E
219
K
PRIO_HUMAN
Polymorphism
1800014
A
E
219
K
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: PRION_2 (A:200-218)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PRION_2
PS00706
Prion protein signature 2.
PRIO_HUMAN
200-218
1
A:200-218
[
close PROSITE info
]
Exons
(1, 1)
Info
All Exons
Exon 1.2e (A:126-222)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.1c/1.2e
2: Boundary 1.2e/-
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
ENST00000379440
1c
ENSE00001957346
chr20:
4666882-4667158
277
PRIO_HUMAN
-
0
0
-
-
1.2e
ENST00000379440
2e
ENSE00001928116
chr20:
4679857-4682236
2380
PRIO_HUMAN
1-257
257
1
A:126-222
97
[
close EXON info
]
SCOP Domains
(3, 3)
Info
All SCOP Domains
1a: SCOP_d4dgil1 (L:1-107)
2a: SCOP_d4dgil2 (L:108-213)
3a: SCOP_d4dgia_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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)
Mouse (Mus musculus) [TaxId: 10090]
(360)
1a
d4dgil1
L:1-107
Family
:
C1 set domains (antibody constant domain-like)
(3013)
Protein domain
:
automated matches
(652)
Mouse (Mus musculus) [TaxId: 10090]
(309)
2a
d4dgil2
L:108-213
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Prion-like
(73)
Superfamily
:
Prion-like
(73)
Family
:
Prion-like
(73)
Protein domain
:
automated matches
(29)
Human (Homo sapiens) [TaxId: 9606]
(8)
3a
d4dgia_
A:
[
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 H
Chain L
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'
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select residue range 5 to 10 in all chains
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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)
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show SS bonds with a radius of 100 units (=0.4Å)
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Asym.Unit (94 KB)
Header - Asym.Unit
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Header - Biol.Unit 1
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