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1KXG
Asym. Unit
Info
Asym.Unit (160 KB)
Biol.Unit 1 (79 KB)
Biol.Unit 2 (79 KB)
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(1)
Title
:
THE 2.0 ANG RESOLUTION STRUCTURE OF BLYS, B LYMPHOCYTE STIMULATOR.
Authors
:
D. A. Oren, Y. Li, Y. Volovik, T. S. Morris, C. Dharia, K. Das, O. Galperina, R. Gentz, E. Arnold
Date
:
31 Jan 02 (Deposition) - 20 Mar 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C (1x)
Biol. Unit 2: D,E,F (1x)
Keywords
:
Baff, Tall-1, Thank, Ztnf4, Cytokine, Tnf Superfamily, Jellyroll, Beta-Sandwich
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. A. Oren, Y. Li, Y. Volovik, T. S. Morris, C. Dharia, K. Das, O. Galperina, R. Gentz, E. Arnold
Structural Basis Of Blys Receptor Recognition.
Nat. Struct. Biol. V. 9 288 2002
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 29)
Info
All Hetero Components
1a: CITRIC ACID (CITa)
1b: CITRIC ACID (CITb)
2a: 1,4-DIETHYLENE DIOXIDE (DIOa)
2b: 1,4-DIETHYLENE DIOXIDE (DIOb)
2c: 1,4-DIETHYLENE DIOXIDE (DIOc)
2d: 1,4-DIETHYLENE DIOXIDE (DIOd)
2e: 1,4-DIETHYLENE DIOXIDE (DIOe)
2f: 1,4-DIETHYLENE DIOXIDE (DIOf)
2g: 1,4-DIETHYLENE DIOXIDE (DIOg)
2h: 1,4-DIETHYLENE DIOXIDE (DIOh)
2i: 1,4-DIETHYLENE DIOXIDE (DIOi)
2j: 1,4-DIETHYLENE DIOXIDE (DIOj)
2k: 1,4-DIETHYLENE DIOXIDE (DIOk)
2l: 1,4-DIETHYLENE DIOXIDE (DIOl)
2m: 1,4-DIETHYLENE DIOXIDE (DIOm)
2n: 1,4-DIETHYLENE DIOXIDE (DIOn)
2o: 1,4-DIETHYLENE DIOXIDE (DIOo)
2p: 1,4-DIETHYLENE DIOXIDE (DIOp)
2q: 1,4-DIETHYLENE DIOXIDE (DIOq)
2r: 1,4-DIETHYLENE DIOXIDE (DIOr)
2s: 1,4-DIETHYLENE DIOXIDE (DIOs)
2t: 1,4-DIETHYLENE DIOXIDE (DIOt)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
3e: MAGNESIUM ION (MGe)
3f: MAGNESIUM ION (MGf)
3g: MAGNESIUM ION (MGg)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CIT
2
Ligand/Ion
CITRIC ACID
2
DIO
20
Ligand/Ion
1,4-DIETHYLENE DIOXIDE
3
MG
7
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(29, 29)
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)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLN A:234 , HOH A:504 , GLN B:234 , MG B:702 , HOH B:1019 , GLN C:234 , HOH C:1017
BINDING SITE FOR RESIDUE MG A 701
02
AC2
SOFTWARE
HOH A:504 , HOH A:507 , MG A:701 , HOH B:1019 , HOH B:1020 , HOH C:1017 , HOH C:1018
BINDING SITE FOR RESIDUE MG B 702
03
AC3
SOFTWARE
MG D:802 , HOH D:1013 , HOH D:1014 , HOH E:1020 , HOH E:1021 , HOH F:603 , HOH F:608
BINDING SITE FOR RESIDUE MG D 801
04
AC4
SOFTWARE
GLN D:234 , MG D:801 , HOH D:1013 , GLN E:234 , HOH E:1020 , GLN F:234 , HOH F:603
BINDING SITE FOR RESIDUE MG D 802
05
AC5
SOFTWARE
HOH A:10 , CIT A:889 , HOH F:395 , CIT F:888
BINDING SITE FOR RESIDUE MG A 901
06
AC6
SOFTWARE
CIT A:889 , ARG F:214 , LYS F:252 , HOH F:395 , CIT F:888
BINDING SITE FOR RESIDUE MG F 902
07
AC7
SOFTWARE
HOH A:10 , ARG A:214 , LYS A:252 , CIT A:889 , CIT F:888
BINDING SITE FOR RESIDUE MG A 903
08
AC8
SOFTWARE
HOH A:4 , HOH A:44 , ARG A:214 , LYS A:252 , CIT A:889 , MG A:901 , MG A:903 , ARG F:214 , LYS F:216 , HIS F:218 , PHE F:220 , GLU F:223 , GLU F:254 , HOH F:344 , MG F:902
BINDING SITE FOR RESIDUE CIT F 888
09
AC9
SOFTWARE
HOH A:2 , ARG A:214 , LYS A:216 , HIS A:218 , PHE A:220 , GLU A:223 , GLU A:254 , HOH A:389 , MG A:901 , MG A:903 , ARG F:214 , LYS F:252 , HOH F:349 , CIT F:888 , MG F:902
BINDING SITE FOR RESIDUE CIT A 889
10
BC1
SOFTWARE
LYS A:160 , PHE A:165 , ASN A:183 , GLN A:260
BINDING SITE FOR RESIDUE DIO A 1001
11
BC2
SOFTWARE
GLN A:234 , SER A:244 , TYR A:246 , SER B:244 , TYR B:246 , TYR C:246
BINDING SITE FOR RESIDUE DIO A 1002
12
BC3
SOFTWARE
LEU A:282 , PHE B:194 , PHE C:194 , LEU C:282
BINDING SITE FOR RESIDUE DIO C 1003
13
BC4
SOFTWARE
HOH A:509 , HOH A:510 , HOH A:511 , HOH C:1020
BINDING SITE FOR RESIDUE DIO A 1004
14
BC5
SOFTWARE
ILE B:158 , PHE B:165 , ASN B:183
BINDING SITE FOR RESIDUE DIO B 1005
15
BC6
SOFTWARE
GLY C:209 , LEU C:211 , ARG C:231 , CYS C:232 , PRO C:264
BINDING SITE FOR RESIDUE DIO C 1006
16
BC7
SOFTWARE
PHE C:165 , ASN C:183 , LYS C:184 , GLN C:260
BINDING SITE FOR RESIDUE DIO C 1007
17
BC8
SOFTWARE
TYR C:192 , LYS C:252 , HOH C:1022 , HIS E:218
BINDING SITE FOR RESIDUE DIO C 1008
18
BC9
SOFTWARE
PHE D:165 , ASN D:183 , GLN D:260
BINDING SITE FOR RESIDUE DIO D 1009
19
CC1
SOFTWARE
PHE D:194 , PHE E:194 , LEU E:282 , LEU F:282
BINDING SITE FOR RESIDUE DIO E 1010
20
CC2
SOFTWARE
PHE E:165 , ASN E:183 , LYS E:184 , GLN E:260
BINDING SITE FOR RESIDUE DIO E 1011
21
CC3
SOFTWARE
TYR D:246 , SER E:244 , TYR E:246 , TYR F:246
BINDING SITE FOR RESIDUE DIO D 1012
22
CC4
SOFTWARE
PHE F:165 , ASN F:183 , LYS F:184
BINDING SITE FOR RESIDUE DIO F 1013
23
CC5
SOFTWARE
ALA C:268 , GLN C:269 , ILE C:270
BINDING SITE FOR RESIDUE DIO C 1014
24
CC6
SOFTWARE
THR A:157 , ALA A:268 , GLN A:269 , ILE A:270
BINDING SITE FOR RESIDUE DIO A 1015
25
CC7
SOFTWARE
HIS C:218 , TYR E:192 , LYS E:252 , HOH F:371
BINDING SITE FOR RESIDUE DIO C 1016
26
CC8
SOFTWARE
LYS A:215 , LYS A:216 , VAL A:217 , GLY A:256 , GLU A:258
BINDING SITE FOR RESIDUE DIO A 1017
27
CC9
SOFTWARE
GLY B:209 , ARG B:231 , PRO B:264
BINDING SITE FOR RESIDUE DIO B 1018
28
DC1
SOFTWARE
THR E:157 , ALA E:268 , GLN E:269 , ILE E:270
BINDING SITE FOR RESIDUE DIO E 1019
29
DC2
SOFTWARE
PRO D:237 , HOH D:1015 , HOH E:1023 , HOH F:423 , HOH F:609
BINDING SITE FOR RESIDUE DIO F 1020
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 6)
Info
All PROSITE Patterns/Profiles
1: TNF_2 (A:148-284,B:148-284,C:148-284,D:14...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TNF_2
PS50049
TNF family profile.
TN13B_HUMAN
148-284
6
A:148-284
B:148-284
C:148-284
D:148-284
E:148-284
F:148-284
[
close PROSITE info
]
Exons
(5, 30)
Info
All Exons
Exon 1.2e (A:142-142 | B:142-142 | C:142-142 ...)
Exon 1.3 (A:142-161 | B:142-161 | C:142-161 ...)
Exon 1.5a (A:161-198 | B:161-198 | C:161-198 ...)
Exon 1.5c (A:199-249 | B:199-249 | C:199-249 ...)
Exon 1.6c (A:249-285 | B:249-285 | C:249-285 ...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.2b/1.2e
2: Boundary 1.2e/1.3
3: Boundary 1.3/1.5a
4: Boundary 1.5a/1.5c
5: Boundary 1.5c/1.6c
6: Boundary 1.6c/-
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
1.2b
ENST00000375887
2b
ENSE00001811977
chr13:
108922066-108922582
517
TN13B_HUMAN
1-113
113
0
-
-
1.2e
ENST00000375887
2e
ENSE00000686291
chr13:
108922688-108922772
85
TN13B_HUMAN
114-142
29
6
A:142-142
B:142-142
C:142-142
D:142-142
E:142-142
F:142-142
1
1
1
1
1
1
1.3
ENST00000375887
3
ENSE00000854068
chr13:
108939151-108939207
57
TN13B_HUMAN
142-161
20
6
A:142-161
B:142-161
C:142-161
D:142-161
E:142-161
F:142-161
20
20
20
20
20
20
1.5a
ENST00000375887
5a
ENSE00000854071
chr13:
108955601-108955713
113
TN13B_HUMAN
161-198
38
6
A:161-198
B:161-198
C:161-198
D:161-198
E:161-198
F:161-198
38
38
38
38
38
38
1.5c
ENST00000375887
5c
ENSE00000854073
chr13:
108955802-108955952
151
TN13B_HUMAN
199-249
51
6
A:199-249
B:199-249
C:199-249
D:199-249
E:199-249
F:199-249
51
51
51
51
51
51
1.6c
ENST00000375887
6c
ENSE00001925016
chr13:
108959174-108959385
212
TN13B_HUMAN
249-285
37
6
A:249-285
B:249-285
C:249-285
D:249-285
E:249-285
F:249-285
37
37
37
37
37
37
[
close EXON info
]
SCOP Domains
(1, 6)
Info
All SCOP Domains
1a: SCOP_d1kxga_ (A:)
1b: SCOP_d1kxgb_ (B:)
1c: SCOP_d1kxgc_ (C:)
1d: SCOP_d1kxgd_ (D:)
1e: SCOP_d1kxge_ (E:)
1f: SCOP_d1kxgf_ (F:)
View:
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Classes
(
)
(
)
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(
)
(
)
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(
)
(
)
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(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
TNF-like
(100)
Superfamily
:
TNF-like
(100)
Family
:
TNF-like
(82)
Protein domain
:
Soluble part of TALL-1, sTALL-1 (BAFF)
(6)
Human (Homo sapiens) [TaxId: 9606]
(6)
1a
d1kxga_
A:
1b
d1kxgb_
B:
1c
d1kxgc_
C:
1d
d1kxgd_
D:
1e
d1kxge_
E:
1f
d1kxgf_
F:
[
close SCOP info
]
CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_1kxgA00 (A:142-285)
1b: CATH_1kxgB00 (B:142-285)
1c: CATH_1kxgC00 (C:142-285)
1d: CATH_1kxgD00 (D:142-285)
1e: CATH_1kxgE00 (E:142-285)
1f: CATH_1kxgF00 (F:142-285)
View:
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Classes
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)
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)
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)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Jelly Rolls
(1293)
Homologous Superfamily
:
[code=2.60.120.40, no name defined]
(56)
Human (Homo sapiens)
(38)
1a
1kxgA00
A:142-285
1b
1kxgB00
B:142-285
1c
1kxgC00
C:142-285
1d
1kxgD00
D:142-285
1e
1kxgE00
E:142-285
1f
1kxgF00
F:142-285
[
close CATH info
]
Pfam Domains
(1, 6)
Info
all PFAM domains
1a: PFAM_TNF_1kxgF01 (F:168-284)
1b: PFAM_TNF_1kxgF02 (F:168-284)
1c: PFAM_TNF_1kxgF03 (F:168-284)
1d: PFAM_TNF_1kxgF04 (F:168-284)
1e: PFAM_TNF_1kxgF05 (F:168-284)
1f: PFAM_TNF_1kxgF06 (F:168-284)
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Clans
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Organisms
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)
Clan
:
C1q_TNF
(45)
Family
:
TNF
(37)
Homo sapiens (Human)
(26)
1a
TNF-1kxgF01
F:168-284
1b
TNF-1kxgF02
F:168-284
1c
TNF-1kxgF03
F:168-284
1d
TNF-1kxgF04
F:168-284
1e
TNF-1kxgF05
F:168-284
1f
TNF-1kxgF06
F:168-284
[
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