PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
1S78
Asym. Unit
Info
Asym.Unit (323 KB)
Biol.Unit 1 (158 KB)
Biol.Unit 2 (161 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
INSIGHTS INTO ERBB SIGNALING FROM THE STRUCTURE OF THE ERBB2-PERTUZUMAB COMPLEX
Authors
:
M. C. Franklin, K. D. Carey, F. F. Vajdos, D. J. Leahy, A. M. De Vos, M. X. S
Date
:
29 Jan 04 (Deposition) - 27 Apr 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.25
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,C,D (1x)
Biol. Unit 2: B,E,F (1x)
Keywords
:
Receptor-Antibody Complex, Fab Fragment, Cysteine-Rich Domain, Leucine-Rich Repeat, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. C. Franklin, K. D. Carey, F. F. Vajdos, D. J. Leahy, A. M. De Vos, M. X. Sliwkowski
Insights Into Erbb Signaling From The Structure Of The Erbb2-Pertuzumab Complex.
Cancer Cell V. 5 317 2004
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 13)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
2a: N-ACETYL-D-GLUCOSAMINE (NAGa)
2b: N-ACETYL-D-GLUCOSAMINE (NAGb)
2c: N-ACETYL-D-GLUCOSAMINE (NAGc)
2d: N-ACETYL-D-GLUCOSAMINE (NAGd)
2e: N-ACETYL-D-GLUCOSAMINE (NAGe)
2f: N-ACETYL-D-GLUCOSAMINE (NAGf)
2g: N-ACETYL-D-GLUCOSAMINE (NAGg)
2h: N-ACETYL-D-GLUCOSAMINE (NAGh)
2i: N-ACETYL-D-GLUCOSAMINE (NAGi)
2j: N-ACETYL-D-GLUCOSAMINE (NAGj)
2k: N-ACETYL-D-GLUCOSAMINE (NAGk)
2l: N-ACETYL-D-GLUCOSAMINE (NAGl)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
1
Ligand/Ion
BETA-D-MANNOSE
2
NAG
12
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(13, 13)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:165 , NAG A:1002 , ASN B:89
BINDING SITE FOR RESIDUE NAG A 1001
02
AC2
SOFTWARE
NAG A:1001
BINDING SITE FOR RESIDUE NAG A 1002
03
AC3
SOFTWARE
ALA A:232 , CYS A:233 , ASN A:237 , NAG A:1004
BINDING SITE FOR RESIDUE NAG A 1003
04
AC4
SOFTWARE
GLN A:32 , NAG A:1003
BINDING SITE FOR RESIDUE NAG A 1004
05
AC5
SOFTWARE
GLN A:462 , VAL A:507 , ASN A:508
BINDING SITE FOR RESIDUE NAG A 1006
06
AC6
SOFTWARE
ASN A:89 , ASN B:165 , NAG B:1002
BINDING SITE FOR RESIDUE NAG B 1001
07
AC7
SOFTWARE
NAG B:1001
BINDING SITE FOR RESIDUE NAG B 1002
08
AC8
SOFTWARE
ALA B:232 , CYS B:233 , ASN B:237 , NAG B:1004
BINDING SITE FOR RESIDUE NAG B 1003
09
AC9
SOFTWARE
GLN B:32 , NAG B:1003 , BMA B:1005 , LYS F:206
BINDING SITE FOR RESIDUE NAG B 1004
10
BC1
SOFTWARE
NAG B:1004
BINDING SITE FOR RESIDUE BMA B 1005
11
BC2
SOFTWARE
GLN B:462 , ASN B:508
BINDING SITE FOR RESIDUE NAG B 1006
12
BC3
SOFTWARE
ASN B:549 , NAG B:1008
BINDING SITE FOR RESIDUE NAG B 1007
13
BC4
SOFTWARE
NAG B:1007
BINDING SITE FOR RESIDUE NAG B 1008
[
close Site info
]
SAPs(SNPs)/Variants
(1, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_016317 (W430C, chain A/B, )
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
A/B
W
430
C
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(15, 30)
Info
All Exons
Exon 1.4 (A:1-3 | B:1-3)
Exon 1.5 (A:3-53 | B:3-53)
Exon 1.6 (A:54-125 (gaps) | B:54-125 (gaps))
Exon 1.7 (A:125-170 | B:125-170)
Exon 1.8 (A:170-193 | B:170-193)
Exon 1.9 (A:193-231 | B:193-231)
Exon 1.10 (A:232-279 | B:232-279)
Exon 1.11 (A:279-319 | B:279-319)
Exon 1.12 (A:319-361 | B:319-361)
Exon 1.13 (A:361-386 | B:361-386)
Exon 1.14 (A:386-416 | B:386-416)
Exon 1.15 (A:416-483 | B:416-483)
Exon 1.16 (A:483-527 | B:483-527)
Exon 1.17 (A:527-557 | B:527-557)
Exon 1.18 (A:558-564 | B:558-577)
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
2
A:1-3
B:1-3
3
3
1.5
ENST00000269571
5
ENSE00001673952
chr17:
37863243-37863394
152
ERBB2_HUMAN
25-75
51
2
A:3-53
B:3-53
51
51
1.6
ENST00000269571
6
ENSE00000950603
chr17:
37864574-37864787
214
ERBB2_HUMAN
76-147
72
2
A:54-125 (gaps)
B:54-125 (gaps)
72
72
1.7
ENST00000269571
7
ENSE00001200960
chr17:
37865571-37865705
135
ERBB2_HUMAN
147-192
46
2
A:125-170
B:125-170
46
46
1.8
ENST00000269571
8
ENSE00001200956
chr17:
37866066-37866134
69
ERBB2_HUMAN
192-215
24
2
A:170-193
B:170-193
24
24
1.9
ENST00000269571
9
ENSE00001200949
chr17:
37866339-37866454
116
ERBB2_HUMAN
215-253
39
2
A:193-231
B:193-231
39
39
1.10
ENST00000269571
10
ENSE00000950607
chr17:
37866593-37866734
142
ERBB2_HUMAN
254-301
48
2
A:232-279
B:232-279
48
48
1.11
ENST00000269571
11
ENSE00001200943
chr17:
37868181-37868300
120
ERBB2_HUMAN
301-341
41
2
A:279-319
B:279-319
41
41
1.12
ENST00000269571
12
ENSE00001200937
chr17:
37868575-37868701
127
ERBB2_HUMAN
341-383
43
2
A:319-361
B:319-361
43
43
1.13
ENST00000269571
13
ENSE00001121108
chr17:
37871539-37871612
74
ERBB2_HUMAN
383-408
26
2
A:361-386
B:361-386
26
26
1.14
ENST00000269571
14
ENSE00001121103
chr17:
37871699-37871789
91
ERBB2_HUMAN
408-438
31
2
A:386-416
B:386-416
31
31
1.15
ENST00000269571
15
ENSE00001121098
chr17:
37871993-37872192
200
ERBB2_HUMAN
438-505
68
2
A:416-483
B:416-483
68
68
1.16
ENST00000269571
16
ENSE00001121093
chr17:
37872554-37872686
133
ERBB2_HUMAN
505-549
45
2
A:483-527
B:483-527
45
45
1.17
ENST00000269571
17
ENSE00001121088
chr17:
37872768-37872858
91
ERBB2_HUMAN
549-579
31
2
A:527-557
B:527-557
31
31
1.18
ENST00000269571
18
ENSE00000950615
chr17:
37873573-37873733
161
ERBB2_HUMAN
580-633
54
2
A:558-564
B:558-577
7
20
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
-
-
[
close EXON info
]
SCOP Domains
(6, 16)
Info
All SCOP Domains
1a: SCOP_d1s78d2 (D:114-216)
1b: SCOP_d1s78f2 (F:114-216)
2a: SCOP_d1s78c2 (C:108-214)
2b: SCOP_d1s78e2 (E:108-214)
3a: SCOP_d1s78d1 (D:1-113)
3b: SCOP_d1s78f1 (F:1-113)
4a: SCOP_d1s78c1 (C:1-107)
4b: SCOP_d1s78e1 (E:1-107)
5a: SCOP_d1s78a1 (A:1-165)
5b: SCOP_d1s78a2 (A:323-488)
5c: SCOP_d1s78b1 (B:1-165)
5d: SCOP_d1s78b2 (B:323-488)
6a: SCOP_d1s78a3 (A:166-322)
6b: SCOP_d1s78a4 (A:489-564)
6c: SCOP_d1s78b3 (B:166-322)
6d: SCOP_d1s78b4 (B:489-577)
View:
Select:
Label:
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
d1s78d2
D:114-216
1b
d1s78f2
F:114-216
Protein domain
:
Immunoglobulin light chain kappa constant domain, CL-kappa
(495)
Human (Homo sapiens) [TaxId: 9606]
(144)
2a
d1s78c2
C:108-214
2b
d1s78e2
E: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
d1s78d1
D:1-113
3b
d1s78f1
F:1-113
Protein domain
:
Immunoglobulin light chain kappa variable domain, VL-kappa
(616)
Engineered (including hybrid species)
(61)
4a
d1s78c1
C:1-107
4b
d1s78e1
E: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
d1s78a1
A:1-165
5b
d1s78a2
A:323-488
5c
d1s78b1
B:1-165
5d
d1s78b2
B: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
d1s78a3
A:166-322
6b
d1s78a4
A:489-564
6c
d1s78b3
B:166-322
6d
d1s78b4
B:489-577
[
close SCOP info
]
CATH Domains
(3, 16)
Info
all CATH domains
1a: CATH_1s78B01 (B:1-163)
1b: CATH_1s78A03 (A:316-510)
1c: CATH_1s78A01 (A:1-203)
1d: CATH_1s78B03 (B:319-486)
2a: CATH_1s78B02 (B:203-312)
2b: CATH_1s78A02 (A:204-315)
2c: CATH_1s78B04 (B:492-577)
2d: CATH_1s78A04 (A:511-564)
3a: CATH_1s78C02 (C:109-211)
3b: CATH_1s78D02 (D:114-213)
3c: CATH_1s78F02 (F:114-213)
3d: CATH_1s78D01 (D:1-113)
3e: CATH_1s78F01 (F:1-113)
3f: CATH_1s78E02 (E:109-211)
3g: CATH_1s78C01 (C:1-108)
3h: CATH_1s78E01 (E:1-108)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
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
1s78B01
B:1-163
1b
1s78A03
A:316-510
1c
1s78A01
A:1-203
1d
1s78B03
B:319-486
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
1s78B02
B:203-312
2b
1s78A02
A:204-315
2c
1s78B04
B:492-577
2d
1s78A04
A:511-564
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
3a
1s78C02
C:109-211
3b
1s78D02
D:114-213
3c
1s78F02
F:114-213
3d
1s78D01
D:1-113
3e
1s78F01
F:1-113
3f
1s78E02
E:109-211
3g
1s78C01
C:1-108
3h
1s78E01
E:1-108
[
close CATH info
]
Pfam Domains
(2, 6)
Info
all PFAM domains
1a: PFAM_Furin_like_1s78B01 (B:161-321)
1b: PFAM_Furin_like_1s78B02 (B:161-321)
2a: PFAM_Recep_L_domain_1s78B03 (B:344-464)
2b: PFAM_Recep_L_domain_1s78B04 (B:344-464)
2c: PFAM_Recep_L_domain_1s78B05 (B:344-464)
2d: PFAM_Recep_L_domain_1s78B06 (B:344-464)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: Furin-like]
(12)
Family
:
Furin-like
(12)
Homo sapiens (Human)
(9)
1a
Furin-like-1s78B01
B:161-321
1b
Furin-like-1s78B02
B:161-321
Clan
:
no clan defined [family: Recep_L_domain]
(12)
Family
:
Recep_L_domain
(12)
Homo sapiens (Human)
(9)
2a
Recep_L_domain-1s78B03
B:344-464
2b
Recep_L_domain-1s78B04
B:344-464
2c
Recep_L_domain-1s78B05
B:344-464
2d
Recep_L_domain-1s78B06
B:344-464
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Chain E
Chain F
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (323 KB)
Header - Asym.Unit
Biol.Unit 1 (158 KB)
Header - Biol.Unit 1
Biol.Unit 2 (161 KB)
Header - Biol.Unit 2
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
1S78
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
