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1ZA3
Asym. Unit
Info
Asym.Unit (175 KB)
Biol.Unit 1 (86 KB)
Biol.Unit 2 (83 KB)
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(1)
Title
:
THE CRYSTAL STRUCTURE OF THE YSD1 FAB BOUND TO DR5
Authors
:
F. A. Fellouse, B. Li, D. M. Compaan, A. A. Peden, S. G. Hymowitz, S. S. Sid
Date
:
05 Apr 05 (Deposition) - 14 Jun 05 (Release) - 05 Feb 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.35
Chains
:
Asym. Unit : A,B,H,L,R,S
Biol. Unit 1: A,B,S (1x)
Biol. Unit 2: H,L,R (1x)
Keywords
:
Phage Display, Protein Engineering, Combinatorial Mutagenesis, Antibody Library, Death Receptor-5, Immune System-Signaling Protein Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
F. A. Fellouse, B. Li, D. M. Compaan, A. A. Peden, S. G. Hymowitz, S. S. Sidhu
Molecular Recognition By A Binary Code.
J. Mol. Biol. V. 348 1153 2005
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Hetero Components
(0, 0)
Info
All Hetero Components
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Sorry, no Info available
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Sites
(0, 0)
Info
All Sites
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Sorry, no Info available
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: TNFR_NGFR_2 (R:43-84,S:43-84|R:85-123,S:85-125)
2: TNFR_NGFR_1 (R:44-84,S:44-84|R:84-123,S:84-125)
;
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TNFR_NGFR_2
PS50050
TNFR/NGFR family cysteine-rich region domain profile.
TR10B_HUMAN
96-137
138-178
4
R:43-84
S:43-84
R:85-123
S:85-125
2
TNFR_NGFR_1
PS00652
TNFR/NGFR family cysteine-rich region signature.
TR10B_HUMAN
97-137
137-178
4
R:44-84
S:44-84
R:84-123
S:84-125
[
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Exons
(4, 8)
Info
All Exons
Exon 1.3a (R:21-31 | S:21-31)
Exon 1.4 (R:31-69 | S:31-69)
Exon 1.5 (R:69-103 | S:69-106)
Exon 1.6c (R:116-123 | S:106-126)
View:
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All Exon Boundaries
1: Boundary 1.1a/1.3a
2: Boundary 1.3a/1.4
3: Boundary 1.4/1.5
4: Boundary 1.5/1.6c
5: Boundary 1.6c/1.7b
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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
ENST00000276431
1a
ENSE00001335538
chr8:
22926692-22926264
429
TR10B_HUMAN
1-48
48
0
-
-
1.3a
ENST00000276431
3a
ENSE00001232611
chr8:
22900756-22900651
106
TR10B_HUMAN
49-84
36
2
R:21-31
S:21-31
11
11
1.4
ENST00000276431
4
ENSE00000980145
chr8:
22888385-22888272
114
TR10B_HUMAN
84-122
39
2
R:31-69
S:31-69
39
39
1.5
ENST00000276431
5
ENSE00000980146
chr8:
22887234-22887123
112
TR10B_HUMAN
122-159
38
2
R:69-103
S:69-106
35
38
1.6c
ENST00000276431
6c
ENSE00001203553
chr8:
22886115-22885844
272
TR10B_HUMAN
159-250
92
2
R:116-123
S:106-126
8
21
1.7b
ENST00000276431
7b
ENSE00000980148
chr8:
22885266-22885235
32
TR10B_HUMAN
250-260
11
0
-
-
1.8b
ENST00000276431
8b
ENSE00001232589
chr8:
22884801-22884646
156
TR10B_HUMAN
261-312
52
0
-
-
1.9
ENST00000276431
9
ENSE00001689788
chr8:
22881773-22881701
73
TR10B_HUMAN
313-337
25
0
-
-
1.10d
ENST00000276431
10d
ENSE00002120034
chr8:
22880497-22877646
2852
TR10B_HUMAN
337-440
104
0
-
-
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SCOP Domains
(5, 14)
Info
All SCOP Domains
1a: SCOP_d1za3b2 (B:114-214)
1b: SCOP_d1za3h2 (H:114-214)
2a: SCOP_d1za3a2 (A:107-213)
2b: SCOP_d1za3l2 (L:107-213)
3a: SCOP_d1za3b1 (B:1-113)
3b: SCOP_d1za3h1 (H:1-113)
4a: SCOP_d1za3a1 (A:1-106)
4b: SCOP_d1za3l1 (L:1-106)
5a: SCOP_d1za3r1 (R:21-61)
5b: SCOP_d1za3r2 (R:62-101)
5c: SCOP_d1za3r3 (R:102-123)
5d: SCOP_d1za3s1 (S:21-61)
5e: SCOP_d1za3s2 (S:62-101)
5f: SCOP_d1za3s3 (S:102-123)
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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
:
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
d1za3b2
B:114-214
1b
d1za3h2
H:114-214
Protein domain
:
Immunoglobulin light chain kappa constant domain, CL-kappa
(495)
Human (Homo sapiens) [TaxId: 9606]
(144)
2a
d1za3a2
A:107-213
2b
d1za3l2
L:107-213
Family
:
V set domains (antibody variable domain-like)
(1919)
Protein domain
:
Camelid IG heavy chain variable domain, VHh
(28)
Human (Homo sapiens) [TaxId: 9606]
(2)
3a
d1za3b1
B:1-113
3b
d1za3h1
H:1-113
Protein domain
:
Immunoglobulin light chain kappa variable domain, VL-kappa
(616)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(9)
4a
d1za3a1
A:1-106
4b
d1za3l1
L:1-106
Class
:
Small proteins
(3458)
Fold
:
TNF receptor-like
(25)
Superfamily
:
TNF receptor-like
(25)
Family
:
TNF receptor-like
(16)
Protein domain
:
Death receptor-5 (dr5) fragment
(5)
Human (Homo sapiens) [TaxId: 9606]
(5)
5a
d1za3r1
R:21-61
5b
d1za3r2
R:62-101
5c
d1za3r3
R:102-123
5d
d1za3s1
S:21-61
5e
d1za3s2
S:62-101
5f
d1za3s3
S:102-123
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CATH Domains
(2, 12)
Info
all CATH domains
1a: CATH_1za3R02 (R:62-101)
1b: CATH_1za3S02 (S:62-101)
1c: CATH_1za3R01 (R:21-61)
1d: CATH_1za3S01 (S:21-61)
2a: CATH_1za3A02 (A:108-213)
2b: CATH_1za3B02 (B:114-214)
2c: CATH_1za3H02 (H:114-214)
2d: CATH_1za3B01 (B:1-113)
2e: CATH_1za3H01 (H:1-113)
2f: CATH_1za3L02 (L:108-213)
2g: CATH_1za3A01 (A:1-107)
2h: CATH_1za3L01 (L:1-107)
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)
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(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Ribbon
(789)
Topology
:
Tumor Necrosis Factor Receptor, subunit A; domain 2
(17)
Homologous Superfamily
:
Tumor Necrosis Factor Receptor, subunit A, domain 2
(16)
[unclassified]
(1)
1a
1za3R02
R:62-101
1b
1za3S02
S:62-101
1c
1za3R01
R:21-61
1d
1za3S01
S:21-61
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
[unclassified]
(54)
2a
1za3A02
A:108-213
2b
1za3B02
B:114-214
2c
1za3H02
H:114-214
2d
1za3B01
B:1-113
2e
1za3H01
H:1-113
2f
1za3L02
L:108-213
2g
1za3A01
A:1-107
2h
1za3L01
L:1-107
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Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_TNFR_c6_1za3S01 (S:44-84)
1b: PFAM_TNFR_c6_1za3S02 (S:44-84)
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Clans
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(
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(
)
(
)
Clan
:
no clan defined [family: TNFR_c6]
(13)
Family
:
TNFR_c6
(13)
Homo sapiens (Human)
(8)
1a
TNFR_c6-1za3S01
S:44-84
1b
TNFR_c6-1za3S02
S:44-84
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