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1N8Z
Asym. Unit
Info
Asym.Unit (166 KB)
Biol.Unit 1 (160 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF EXTRACELLULAR DOMAIN OF HUMAN HER2 COMPLEXED WITH HERCEPTIN FAB
Authors
:
H. -S. Cho, K. Mason, K. X. Ramyar, A. M. Stanley, S. B. Gabelli, D. W. Denn D. J. Leahy
Date
:
21 Nov 02 (Deposition) - 18 Feb 03 (Release) - 05 Feb 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.52
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (1x)
Keywords
:
Tyrosin Kinase Receptor, Cell Surface Receptor, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. -S. Cho, K. Mason, K. X. Ramyar, A. M. Stanley, S. B. Gabelli, D. W. Denney Jr. , D. J. Leahy
Structure Of The Extracellular Region Of Her2 Alone And In Complex With The Herceptin Fab
Nature V. 421 756 2003
[
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Hetero Components
(2, 3)
Info
All Hetero Components
1a: N-ACETYL-D-GLUCOSAMINE (NAGa)
1b: N-ACETYL-D-GLUCOSAMINE (NAGb)
2a: SULFATE ION (SO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAG
2
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
2
SO4
1
Ligand/Ion
SULFATE ION
[
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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
GLU A:123 , SER B:127 , VAL B:128 , VAL B:214 , LYS B:216 , ASN C:165 , ARG C:166 , SER C:167
BINDING SITE FOR RESIDUE NAG C 766
2
AC2
SOFTWARE
PHE B:27 , ASN B:28 , CYS C:230 , ASN C:237
BINDING SITE FOR RESIDUE NAG C 738
3
AC3
SOFTWARE
HIS C:456 , HIS C:473 , THR C:474 , ASN C:476
BINDING SITE FOR RESIDUE SO4 C 1001
[
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SAPs(SNPs)/Variants
(1, 1)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_016317 (W430C, chain C, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_016317
W
452
C
ERBB2_HUMAN
Polymorphism
4252633
C
W
430
C
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
End label:
Sorry, no Info available
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Exons
(15, 15)
Info
All Exons
Exon 1.4 (C:1-3)
Exon 1.5 (C:3-53)
Exon 1.6 (C:54-125 (gaps))
Exon 1.7 (C:125-170)
Exon 1.8 (C:170-193)
Exon 1.9 (C:193-231)
Exon 1.10 (C:232-279)
Exon 1.11 (C:279-319 (gaps))
Exon 1.12 (C:319-360)
Exon 1.13 (C:365-386)
Exon 1.14 (C:386-416)
Exon 1.15 (C:416-483)
Exon 1.16 (C:483-527)
Exon 1.17 (C:527-557)
Exon 1.18 (C:558-607 (gaps))
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.4
02: Boundary 1.4/1.5
03: Boundary 1.5/1.6
04: Boundary 1.6/1.7
05: Boundary 1.7/1.8
06: Boundary 1.8/1.9
07: Boundary 1.9/1.10
08: Boundary 1.10/1.11
09: Boundary 1.11/1.12
10: Boundary 1.12/1.13
11: Boundary 1.13/1.14
12: Boundary 1.14/1.15
13: Boundary 1.15/1.16
14: Boundary 1.16/1.17
15: Boundary 1.17/1.18
16: Boundary 1.18/1.19
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
1.4
ENST00000269571
4
ENSE00001234770
chr17:
37856254-37856564
311
ERBB2_HUMAN
1-25
25
1
C:1-3
3
1.5
ENST00000269571
5
ENSE00001673952
chr17:
37863243-37863394
152
ERBB2_HUMAN
25-75
51
1
C:3-53
51
1.6
ENST00000269571
6
ENSE00000950603
chr17:
37864574-37864787
214
ERBB2_HUMAN
76-147
72
1
C:54-125 (gaps)
72
1.7
ENST00000269571
7
ENSE00001200960
chr17:
37865571-37865705
135
ERBB2_HUMAN
147-192
46
1
C:125-170
46
1.8
ENST00000269571
8
ENSE00001200956
chr17:
37866066-37866134
69
ERBB2_HUMAN
192-215
24
1
C:170-193
24
1.9
ENST00000269571
9
ENSE00001200949
chr17:
37866339-37866454
116
ERBB2_HUMAN
215-253
39
1
C:193-231
39
1.10
ENST00000269571
10
ENSE00000950607
chr17:
37866593-37866734
142
ERBB2_HUMAN
254-301
48
1
C:232-279
48
1.11
ENST00000269571
11
ENSE00001200943
chr17:
37868181-37868300
120
ERBB2_HUMAN
301-341
41
1
C:279-319 (gaps)
41
1.12
ENST00000269571
12
ENSE00001200937
chr17:
37868575-37868701
127
ERBB2_HUMAN
341-383
43
1
C:319-360
42
1.13
ENST00000269571
13
ENSE00001121108
chr17:
37871539-37871612
74
ERBB2_HUMAN
383-408
26
1
C:365-386
22
1.14
ENST00000269571
14
ENSE00001121103
chr17:
37871699-37871789
91
ERBB2_HUMAN
408-438
31
1
C:386-416
31
1.15
ENST00000269571
15
ENSE00001121098
chr17:
37871993-37872192
200
ERBB2_HUMAN
438-505
68
1
C:416-483
68
1.16
ENST00000269571
16
ENSE00001121093
chr17:
37872554-37872686
133
ERBB2_HUMAN
505-549
45
1
C:483-527
45
1.17
ENST00000269571
17
ENSE00001121088
chr17:
37872768-37872858
91
ERBB2_HUMAN
549-579
31
1
C:527-557
31
1.18
ENST00000269571
18
ENSE00000950615
chr17:
37873573-37873733
161
ERBB2_HUMAN
580-633
54
1
C:558-607 (gaps)
50
1.19
ENST00000269571
19
ENSE00001121079
chr17:
37876040-37876087
48
ERBB2_HUMAN
633-649
17
0
-
-
1.20
ENST00000269571
20
ENSE00001121070
chr17:
37879572-37879710
139
ERBB2_HUMAN
649-695
47
0
-
-
1.21
ENST00000269571
21
ENSE00000950618
chr17:
37879791-37879913
123
ERBB2_HUMAN
696-736
41
0
-
-
1.22
ENST00000269571
22
ENSE00000950619
chr17:
37880165-37880263
99
ERBB2_HUMAN
737-769
33
0
-
-
1.23
ENST00000269571
23
ENSE00000950620
chr17:
37880979-37881164
186
ERBB2_HUMAN
770-831
62
0
-
-
1.24
ENST00000269571
24
ENSE00000950621
chr17:
37881302-37881457
156
ERBB2_HUMAN
832-883
52
0
-
-
1.25
ENST00000269571
25
ENSE00001717073
chr17:
37881580-37881655
76
ERBB2_HUMAN
884-909
26
0
-
-
1.26
ENST00000269571
26
ENSE00000950623
chr17:
37881960-37882106
147
ERBB2_HUMAN
909-958
50
0
-
-
1.27
ENST00000269571
27
ENSE00000950624
chr17:
37882815-37882912
98
ERBB2_HUMAN
958-990
33
0
-
-
1.28
ENST00000269571
28
ENSE00000950625
chr17:
37883068-37883256
189
ERBB2_HUMAN
991-1053
63
0
-
-
1.29
ENST00000269571
29
ENSE00000950626
chr17:
37883548-37883800
253
ERBB2_HUMAN
1054-1138
85
0
-
-
1.30
ENST00000269571
30
ENSE00001384235
chr17:
37883942-37884915
974
ERBB2_HUMAN
1138-1255
118
0
-
-
[
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]
SCOP Domains
(6, 8)
Info
All SCOP Domains
1a: SCOP_d1n8zb2 (B:121-220)
2a: SCOP_d1n8za2 (A:108-214)
3a: SCOP_d1n8zb1 (B:1-120)
4a: SCOP_d1n8za1 (A:1-107)
5a: SCOP_d1n8zc1 (C:1-165)
5b: SCOP_d1n8zc2 (C:323-488)
6a: SCOP_d1n8zc3 (C:166-322)
6b: SCOP_d1n8zc4 (C:489-607)
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(
)
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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
d1n8zb2
B:121-220
Protein domain
:
Immunoglobulin light chain kappa constant domain, CL-kappa
(495)
Human (Homo sapiens) [TaxId: 9606]
(144)
2a
d1n8za2
A:108-214
Family
:
V set domains (antibody variable domain-like)
(1919)
Protein domain
:
Immunoglobulin heavy chain variable domain, VH
(658)
Engineered (including hybrid species)
(68)
3a
d1n8zb1
B:1-120
Protein domain
:
Immunoglobulin light chain kappa variable domain, VL-kappa
(616)
Engineered (including hybrid species)
(61)
4a
d1n8za1
A:1-107
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
(112)
Superfamily
:
L domain-like
(93)
Family
:
L domain
(16)
Protein domain
:
Protooncoprotein Her2 extracellular domain
(3)
Human (Homo sapiens) [TaxId: 9606]
(2)
5a
d1n8zc1
C:1-165
5b
d1n8zc2
C:323-488
Class
:
Small proteins
(3458)
Fold
:
Knottins (small inhibitors, toxins, lectins)
(761)
Superfamily
:
Growth factor receptor domain
(25)
Family
:
Growth factor receptor domain
(18)
Protein domain
:
Protooncoprotein Her2 extracellular domain
(3)
Human (Homo sapiens) [TaxId: 9606]
(2)
6a
d1n8zc3
C:166-322
6b
d1n8zc4
C:489-607
[
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]
CATH Domains
(3, 8)
Info
all CATH domains
1a: CATH_1n8zC01 (C:1-192)
1b: CATH_1n8zC03 (C:317-484)
2a: CATH_1n8zC02 (C:193-316)
2b: CATH_1n8zC04 (C:485-607)
3a: CATH_1n8zA02 (A:109-211)
3b: CATH_1n8zB02 (B:121-220)
3c: CATH_1n8zB01 (B:1-120)
3d: CATH_1n8zA01 (A:1-108)
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Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Horseshoe
(92)
Topology
:
24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A
(17)
Homologous Superfamily
:
24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'. Chain A, domain 1
(17)
Human (Homo sapiens)
(14)
1a
1n8zC01
C:1-192
1b
1n8zC03
C:317-484
Class
:
Mainly Beta
(13760)
Architecture
:
Ribbon
(789)
Topology
:
Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2
(15)
Homologous Superfamily
:
Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2
(15)
Human (Homo sapiens)
(13)
2a
1n8zC02
C:193-316
2b
1n8zC04
C:485-607
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
3a
1n8zA02
A:109-211
3b
1n8zB02
B:121-220
3c
1n8zB01
B:1-120
3d
1n8zA01
A:1-108
[
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Pfam Domains
(2, 3)
Info
all PFAM domains
1a: PFAM_Furin_like_1n8zC01 (C:161-321)
2a: PFAM_Recep_L_domain_1n8zC02 (C:344-464)
2b: PFAM_Recep_L_domain_1n8zC03 (C:344-464)
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Clans
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(
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Families
(
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(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: Furin-like]
(12)
Family
:
Furin-like
(12)
Homo sapiens (Human)
(9)
1a
Furin-like-1n8zC01
C:161-321
Clan
:
no clan defined [family: Recep_L_domain]
(12)
Family
:
Recep_L_domain
(12)
Homo sapiens (Human)
(9)
2a
Recep_L_domain-1n8zC02
C:344-464
2b
Recep_L_domain-1n8zC03
C:344-464
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Asymmetric Unit 1
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Asym.Unit (166 KB)
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