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Getting 'Exon' information from database.
3D85
Asym. Unit
Info
Asym.Unit (160 KB)
Biol.Unit 1 (154 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF IL-23 IN COMPLEX WITH NEUTRALIZING FAB
Authors
:
B. M. Beyer, R. Ingram, L. Ramanathan, P. Reichert, H. Le, V. Madison
Date
:
22 May 08 (Deposition) - 02 Sep 08 (Release) - 23 Dec 08 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Interleukin-23, Fab, Immune System/Cytokine Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. M. Beyer, R. Ingram, L. Ramanathan, P. Reichert, H. V. Le, V. Madison, P. Orth
Crystal Structures Of The Pro-Inflammatory Cytokine Interleukin-23 And Its Complex With A High-Affinity Neutralizing Antibody
J. Mol. Biol. V. 382 942 2008
(for further references see the
PDB file header
)
[
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Hetero Components
(2, 3)
Info
All Hetero Components
1a: IMIDAZOLE (IMDa)
2a: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDa)
2b: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
IMD
1
Ligand/Ion
IMIDAZOLE
2
MPD
2
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
[
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Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
THR B:30 , SER B:31 , TYR B:54 , HIS C:106
BINDING SITE FOR RESIDUE MPD B 501
2
AC2
SOFTWARE
GLN A:155 , LEU A:181 , HIS A:189
BINDING SITE FOR RESIDUE MPD A 502
[
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SAPs(SNPs)/Variants
(4, 4)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_020001 (V11I, chain D, )
2: VAR_066403 (W148R, chain A, )
3: VAR_003897 (V191L, chain A, )
4: VAR_049170 (V276F, chain D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_020001
V
33
I
IL12B_HUMAN
Polymorphism
3213096
D
V
11
I
2
UniProt
VAR_066403
W
40
R
IGKC_HUMAN
Disease (IGKCD)
---
A
W
148
R
3
UniProt
VAR_003897
V
83
L
IGKC_HUMAN
Unclassified
---
A
V
191
L
4
UniProt
VAR_049170
V
298
F
IL12B_HUMAN
Polymorphism
3213119
D
V
276
F
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(3, 3)
Info
All PROSITE Patterns/Profiles
1: IG_MHC (A:192-198)
2: HEMATOPO_REC_L_F3 (D:211-253)
3: FN3 (D:215-305)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
IG_MHC
PS00290
Immunoglobulins and major histocompatibility complex proteins signature.
IGKC_HUMAN
85-91
1
A:192-198
2
HEMATOPO_REC_L_F3
PS01354
Long hematopoietin receptor, soluble alpha chains family signature.
IL12B_HUMAN
233-275
1
D:211-253
3
FN3
PS50853
Fibronectin type-III domain profile.
IL12B_HUMAN
237-328
1
D:215-305
[
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]
Exons
(6, 6)
Info
All Exons
Exon 1.2 (D:1-8)
Exon 1.3 (D:8-99)
Exon 1.4 (D:103-139)
Exon 1.5 (D:139-211 (gaps))
Exon 1.6 (D:211-257 (gaps))
Exon 1.7 (D:264-305)
View:
Select:
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All Exon Boundaries
1: Boundary 1.1/1.2
2: Boundary 1.2/1.3
3: Boundary 1.3/1.4
4: Boundary 1.4/1.5
5: Boundary 1.5/1.6
6: Boundary 1.6/1.7
7: Boundary 1.7/1.8
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
1.1
ENST00000231228
1
ENSE00001230769
chr5:
158757895-158757440
456
IL12B_HUMAN
-
0
0
-
-
1.2
ENST00000231228
2
ENSE00000797276
chr5:
158753790-158753703
88
IL12B_HUMAN
1-30
30
1
D:1-8
8
1.3
ENST00000231228
3
ENSE00000768666
chr5:
158750337-158750062
276
IL12B_HUMAN
30-122
93
1
D:8-99
92
1.4
ENST00000231228
4
ENSE00000768664
chr5:
158749519-158749402
118
IL12B_HUMAN
122-161
40
1
D:103-139
37
1.5
ENST00000231228
5
ENSE00000768662
chr5:
158747528-158747314
215
IL12B_HUMAN
161-233
73
1
D:139-211 (gaps)
73
1.6
ENST00000231228
6
ENSE00000768660
chr5:
158745901-158745744
158
IL12B_HUMAN
233-285
53
1
D:211-257 (gaps)
47
1.7
ENST00000231228
7
ENSE00001371782
chr5:
158743824-158743693
132
IL12B_HUMAN
286-328
43
1
D:264-305
42
1.8
ENST00000231228
8
ENSE00000797274
chr5:
158743108-158741791
1318
IL12B_HUMAN
-
0
0
-
-
[
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SCOP Domains
(4, 5)
Info
All SCOP Domains
1a: SCOP_d3d85d2 (D:88-211)
1b: SCOP_d3d85d3 (D:212-305)
2a: SCOP_d3d85a1 (A:1-107)
3a: SCOP_d3d85a2 (A:108-213)
4a: SCOP_d3d85d1 (D:1-87)
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Classes
(
)
(
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(
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Fibronectin type III
(212)
Family
:
Fibronectin type III
(180)
Protein domain
:
The p40 domain of interleukin-12 (IL-12 beta chain), domains 2 and 3
(5)
Human (Homo sapiens) [TaxId: 9606]
(5)
1a
d3d85d2
D:88-211
1b
d3d85d3
D:212-305
Superfamily
:
Immunoglobulin
(5995)
Family
:
automated matches
(864)
Protein domain
:
automated matches
(864)
Human (Homo sapiens) [TaxId: 9606]
(448)
2a
d3d85a1
A:1-107
Family
:
C1 set domains (antibody constant domain-like)
(3013)
Protein domain
:
automated matches
(652)
Human (Homo sapiens) [TaxId: 9606]
(334)
3a
d3d85a2
A:108-213
Family
:
I set domains
(152)
Protein domain
:
The p40 domain of interleukin-12 (IL-12 beta chain), N-terminal domain
(5)
Human (Homo sapiens) [TaxId: 9606]
(5)
4a
d3d85d1
D:1-87
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CATH Domains
(1, 7)
Info
all CATH domains
1a: CATH_3d85A02 (A:109-213)
1b: CATH_3d85B02 (B:116-215)
1c: CATH_3d85B01 (B:1-115)
1d: CATH_3d85D02 (D:103-210)
1e: CATH_3d85D01 (D:1-84)
1f: CATH_3d85D03 (D:214-304)
1g: CATH_3d85A01 (A:1-108)
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(
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Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
1a
3d85A02
A:109-213
1b
3d85B02
B:116-215
1c
3d85B01
B:1-115
1d
3d85D02
D:103-210
1e
3d85D01
D:1-84
1f
3d85D03
D:214-304
1g
3d85A01
A:1-108
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
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Protein & NOT PROSITE
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Chain D
Asymmetric Unit 1
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