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1I9R
Asym. Unit
Info
Asym.Unit (274 KB)
Biol.Unit 1 (267 KB)
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(1)
Title
:
STRUCTURE OF CD40L IN COMPLEX WITH THE FAB FRAGMENT OF HUMANIZED 5C8 ANTIBODY
Authors
:
M. Karpusas, J. Lucci, J. Ferrant, C. Benjamin, Y. -M. Hsu
Date
:
20 Mar 01 (Deposition) - 20 Mar 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.10
Chains
:
Asym. Unit : A,B,C,H,K,L,M,X,Y
Biol. Unit 1: A,B,C,H,K,L,M,X,Y (1x)
Keywords
:
Beta-Sheet Sandwich, Immunoglobulin, Cytokine/Immune System Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Karpusas, J. Lucci, J. Ferrant, C. Benjamin, F. R. Taylor, K. Strauch, E. Garber, Y. M. Hsu
Structure Of Cd40 Ligand In Complex With The Fab Fragment Of A Neutralizing Humanized Antibody.
Structure V. 9 321 2001
(for further references see the
PDB file header
)
[
close entry info
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Hetero Components
(1, 3)
Info
All Hetero Components
1a: ZINC ION (ZNa)
1b: ZINC ION (ZNb)
1c: ZINC ION (ZNc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ZN
3
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP H:100 , ASP H:104 , ASP H:106 , LYS L:53 , GLU L:59
BINDING SITE FOR RESIDUE ZN H 498
2
AC2
SOFTWARE
ASP K:100 , ASP K:104 , ASP K:106 , LYS M:53 , GLU M:59
BINDING SITE FOR RESIDUE ZN K 499
3
AC3
SOFTWARE
ASP X:100 , ASP X:104 , ASP X:106 , LYS Y:53 , GLU Y:59
BINDING SITE FOR RESIDUE ZN X 500
[
close Site info
]
SAPs(SNPs)/Variants
(29, 87)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_007514 (A123E, chain A/B/C, )
02: VAR_017926 (H125R, chain A/B/C, )
03: VAR_007515 (V126A, chain A/B/C, )
04: VAR_017931 (V126D, chain A/B/C, )
05: VAR_007517 (W140C, chain A/B/C, )
06: VAR_007518 (W140G, chain A/B/C, )
07: VAR_007519 (W140R, chain A/B/C, )
08: VAR_017932 (K143T, chain A/B/C, )
09: VAR_007520 (G144E, chain A/B/C, )
10: VAR_017922 (T147N, chain A/B/C, )
11: VAR_007521 (L155P, chain A/B/C, )
12: VAR_017923 (Y170C, chain A/B/C, )
13: VAR_017933 (A173D, chain A/B/C, )
14: VAR_017927 (Q174R, chain A/B/C, )
15: VAR_017934 (T176I, chain A/B/C, )
16: VAR_017935 (L195P, chain A/B/C, )
17: VAR_017936 (A208D, chain A/B/C, )
18: VAR_007522 (T211N, chain A/B/C, )
19: VAR_007523 (G219R, chain A/B/C, )
20: VAR_017937 (H224Y, chain A/B/C, )
21: VAR_017938 (G226A, chain A/B/C, )
22: VAR_007524 (G227V, chain A/B/C, )
23: VAR_007526 (L231S, chain A/B/C, )
24: VAR_007527 (A235P, chain A/B/C, )
25: VAR_017939 (V237E, chain A/B/C, )
26: VAR_007528 (T254M, chain A/B/C, )
27: VAR_017940 (G257D, chain A/B/C, )
28: VAR_017928 (G257S, chain A/B/C, )
29: VAR_017924 (L258S, chain A/B/C, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_007514
A
123
E
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
A
123
E
02
UniProt
VAR_017926
H
125
R
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
H
125
R
03
UniProt
VAR_007515
V
126
A
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
V
126
A
04
UniProt
VAR_017931
V
126
D
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
V
126
D
05
UniProt
VAR_007517
W
140
C
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
W
140
C
06
UniProt
VAR_007518
W
140
G
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
W
140
G
07
UniProt
VAR_007519
W
140
R
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
W
140
R
08
UniProt
VAR_017932
K
143
T
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
K
143
T
09
UniProt
VAR_007520
G
144
E
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
G
144
E
10
UniProt
VAR_017922
T
147
N
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
T
147
N
11
UniProt
VAR_007521
L
155
P
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
L
155
P
12
UniProt
VAR_017923
Y
170
C
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
Y
170
C
13
UniProt
VAR_017933
A
173
D
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
A
173
D
14
UniProt
VAR_017927
Q
174
R
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
Q
174
R
15
UniProt
VAR_017934
T
176
I
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
T
176
I
16
UniProt
VAR_017935
L
195
P
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
L
195
P
17
UniProt
VAR_017936
A
208
D
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
A
208
D
18
UniProt
VAR_007522
T
211
N
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
T
211
N
19
UniProt
VAR_007523
G
219
R
CD40L_HUMAN
Polymorphism
148594123
A/B/C
G
219
R
20
UniProt
VAR_017937
H
224
Y
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
H
224
Y
21
UniProt
VAR_017938
G
226
A
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
G
226
A
22
UniProt
VAR_007524
G
227
V
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
G
227
V
23
UniProt
VAR_007526
L
231
S
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
L
231
S
24
UniProt
VAR_007527
A
235
P
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
A
235
P
25
UniProt
VAR_017939
V
237
E
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
V
237
E
26
UniProt
VAR_007528
T
254
M
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
T
254
M
27
UniProt
VAR_017940
G
257
D
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
G
257
D
28
UniProt
VAR_017928
G
257
S
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
G
257
S
29
UniProt
VAR_017924
L
258
S
CD40L_HUMAN
Disease (HIGM1)
---
A/B/C
L
258
S
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 6)
Info
All PROSITE Patterns/Profiles
1: TNF_2 (A:123-261,B:123-261,C:123-261)
2: TNF_1 (A:161-177,B:161-177,C:161-177)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TNF_2
PS50049
TNF family profile.
CD40L_HUMAN
123-261
3
A:123-261
B:123-261
C:123-261
2
TNF_1
PS00251
TNF family signature.
CD40L_HUMAN
161-177
3
A:161-177
B:161-177
C:161-177
[
close PROSITE info
]
Exons
(2, 6)
Info
All Exons
Exon 1.4 (A:119-137 | B:119-137 | C:119-137)
Exon 1.5 (A:137-261 | B:137-261 | C:137-261)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.3/1.4
2: Boundary 1.4/1.5
3: Boundary 1.5/-
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
1.1a
ENST00000370629
1a
ENSE00001453187
X:135730352-135730563
212
CD40L_HUMAN
1-52
52
0
-
-
1.2
ENST00000370629
2
ENSE00000677016
X:135732425-135732556
132
CD40L_HUMAN
53-96
44
0
-
-
1.3
ENST00000370629
3
ENSE00000677017
X:135736532-135736589
58
CD40L_HUMAN
97-116
20
0
-
-
1.4
ENST00000370629
4
ENSE00000677018
X:135738515-135738577
63
CD40L_HUMAN
116-137
22
3
A:119-137
B:119-137
C:119-137
19
19
19
1.5
ENST00000370629
5
ENSE00001125156
X:135741198-135742549
1352
CD40L_HUMAN
137-261
125
3
A:137-261
B:137-261
C:137-261
125
125
125
[
close EXON info
]
SCOP Domains
(5, 15)
Info
All SCOP Domains
1a: SCOP_d1i9rh2 (H:119-219)
1b: SCOP_d1i9rk2 (K:119-219)
1c: SCOP_d1i9rx2 (X:119-219)
2a: SCOP_d1i9rl2 (L:112-215)
2b: SCOP_d1i9rm2 (M:112-215)
2c: SCOP_d1i9ry2 (Y:112-215)
3a: SCOP_d1i9rh1 (H:1-118)
3b: SCOP_d1i9rk1 (K:1-118)
3c: SCOP_d1i9rx1 (X:1-118)
4a: SCOP_d1i9rl1 (L:1-111)
4b: SCOP_d1i9rm1 (M:1-111)
4c: SCOP_d1i9ry1 (Y:1-111)
5a: SCOP_d1i9ra_ (A:)
5b: SCOP_d1i9rb_ (B:)
5c: SCOP_d1i9rc_ (C:)
View:
Select:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Immunoglobulin
(5995)
Family
:
C1 set domains (antibody constant domain-like)
(3013)
Protein domain
:
Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma
(608)
Human (Homo sapiens) [TaxId: 9606]
(179)
1a
d1i9rh2
H:119-219
1b
d1i9rk2
K:119-219
1c
d1i9rx2
X:119-219
Protein domain
:
Immunoglobulin light chain kappa constant domain, CL-kappa
(495)
Human (Homo sapiens) [TaxId: 9606]
(144)
2a
d1i9rl2
L:112-215
2b
d1i9rm2
M:112-215
2c
d1i9ry2
Y:112-215
Family
:
V set domains (antibody variable domain-like)
(1919)
Protein domain
:
Immunoglobulin heavy chain variable domain, VH
(658)
Engineered (including hybrid species)
(68)
3a
d1i9rh1
H:1-118
3b
d1i9rk1
K:1-118
3c
d1i9rx1
X:1-118
Protein domain
:
Immunoglobulin light chain kappa variable domain, VL-kappa
(616)
Engineered (including hybrid species)
(61)
4a
d1i9rl1
L:1-111
4b
d1i9rm1
M:1-111
4c
d1i9ry1
Y:1-111
Fold
:
TNF-like
(100)
Superfamily
:
TNF-like
(100)
Family
:
TNF-like
(82)
Protein domain
:
Extracellular domain of CD40 ligand
(2)
Human (Homo sapiens) [TaxId: 9606]
(2)
5a
d1i9ra_
A:
5b
d1i9rb_
B:
5c
d1i9rc_
C:
[
close SCOP info
]
CATH Domains
(2, 15)
Info
all CATH domains
1a: CATH_1i9rL02 (L:113-215)
1b: CATH_1i9rL01 (L:1-112)
1c: CATH_1i9rM01 (M:1-112)
1d: CATH_1i9rY01 (Y:1-112)
1e: CATH_1i9rH02 (H:113-219)
1f: CATH_1i9rK02 (K:113-219)
1g: CATH_1i9rX02 (X:113-219)
1h: CATH_1i9rH01 (H:1-112)
1i: CATH_1i9rK01 (K:1-112)
1j: CATH_1i9rX01 (X:1-112)
1k: CATH_1i9rM02 (M:113-215)
1l: CATH_1i9rY02 (Y:113-215)
2a: CATH_1i9rA00 (A:119-261)
2b: CATH_1i9rB00 (B:119-261)
2c: CATH_1i9rC00 (C:119-261)
View:
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Classes
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)
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)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
1a
1i9rL02
L:113-215
1b
1i9rL01
L:1-112
1c
1i9rM01
M:1-112
1d
1i9rY01
Y:1-112
1e
1i9rH02
H:113-219
1f
1i9rK02
K:113-219
1g
1i9rX02
X:113-219
1h
1i9rH01
H:1-112
1i
1i9rK01
K:1-112
1j
1i9rX01
X:1-112
1k
1i9rM02
M:113-215
1l
1i9rY02
Y:113-215
Topology
:
Jelly Rolls
(1293)
Homologous Superfamily
:
[code=2.60.120.40, no name defined]
(56)
Human (Homo sapiens)
(38)
2a
1i9rA00
A:119-261
2b
1i9rB00
B:119-261
2c
1i9rC00
C:119-261
[
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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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