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.
1YY9
Asym. Unit
Info
Asym.Unit (174 KB)
Biol.Unit 1 (166 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF THE EXTRACELLULAR DOMAIN OF THE EPIDERMAL GROWTH FACTOR RECEPTOR IN COMPLEX WITH THE FAB FRAGMENT OF CETUXIMAB/ERBITUX/IMC-C225
Authors
:
S. Li, K. R. Schmitz, P. D. Jeffrey, J. J. W. Wiltzius, P. Kussie, K. M. Fer
Date
:
24 Feb 05 (Deposition) - 26 Apr 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,C,D
Biol. Unit 1: A,C,D (1x)
Keywords
:
Cell Surface Receptor; Tyrosine Kinase; Glycoprotein; Antigen:Antibody Complex; Fab Fragment; Antitumor; Drug, Immune System-Transferase Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Li, K. R. Schmitz, P. D. Jeffrey, J. J. W. Wiltzius, P. Kussie, K. M. Ferguson
Structural Basis For Inhibition Of The Epidermal Growth Factor Receptor By Cetuximab
Cancer Cell V. 7 301 2005
[
close entry info
]
Hetero Components
(4, 20)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
2a: ALPHA-D-MANNOSE (MANa)
2b: ALPHA-D-MANNOSE (MANb)
2c: ALPHA-D-MANNOSE (MANc)
2d: ALPHA-D-MANNOSE (MANd)
2e: ALPHA-D-MANNOSE (MANe)
2f: ALPHA-D-MANNOSE (MANf)
3a: N-ACETYL-D-GLUCOSAMINE (NAGa)
3b: N-ACETYL-D-GLUCOSAMINE (NAGb)
3c: N-ACETYL-D-GLUCOSAMINE (NAGc)
3d: N-ACETYL-D-GLUCOSAMINE (NAGd)
3e: N-ACETYL-D-GLUCOSAMINE (NAGe)
3f: N-ACETYL-D-GLUCOSAMINE (NAGf)
3g: N-ACETYL-D-GLUCOSAMINE (NAGg)
3h: N-ACETYL-D-GLUCOSAMINE (NAGh)
3i: N-ACETYL-D-GLUCOSAMINE (NAGi)
3j: N-ACETYL-D-GLUCOSAMINE (NAGj)
3k: N-ACETYL-D-GLUCOSAMINE (NAGk)
4a: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGa)
4b: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
1
Ligand/Ion
BETA-D-MANNOSE
2
MAN
6
Ligand/Ion
ALPHA-D-MANNOSE
3
NAG
11
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
4
NDG
2
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
[
close Hetero Component info
]
Sites
(20, 20)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:32 , ASN A:33
BINDING SITE FOR RESIDUE NDG A 625
02
AC2
SOFTWARE
ASN D:88
BINDING SITE FOR RESIDUE NDG D 881
03
AC3
SOFTWARE
SER A:324 , LEU A:325 , SER A:326 , ASN A:328 , ASN A:331 , ASP A:355 , THR A:358 , THR A:360 , NAG A:3282
BINDING SITE FOR RESIDUE NAG A 3281
04
AC4
SOFTWARE
ASP A:323 , NAG A:3281 , BMA A:3283
BINDING SITE FOR RESIDUE NAG A 3282
05
AC5
SOFTWARE
ASP A:323 , NAG A:3282 , MAN A:3284 , MAN A:3285
BINDING SITE FOR RESIDUE BMA A 3283
06
AC6
SOFTWARE
BMA A:3283 , MAN A:3287 , MAN A:3289
BINDING SITE FOR RESIDUE MAN A 3284
07
AC7
SOFTWARE
BMA A:3283 , MAN A:3286
BINDING SITE FOR RESIDUE MAN A 3285
08
AC8
SOFTWARE
MAN A:3285
BINDING SITE FOR RESIDUE MAN A 3286
09
AC9
SOFTWARE
MAN A:3284 , MAN A:3288
BINDING SITE FOR RESIDUE MAN A 3287
10
BC1
SOFTWARE
MAN A:3287
BINDING SITE FOR RESIDUE MAN A 3288
11
BC2
SOFTWARE
MAN A:3284
BINDING SITE FOR RESIDUE MAN A 3289
12
BC3
SOFTWARE
LYS A:311 , LYS A:336 , ASN A:337 , NAG A:3372
BINDING SITE FOR RESIDUE NAG A 3371
13
BC4
SOFTWARE
NAG A:3371
BINDING SITE FOR RESIDUE NAG A 3372
14
BC5
SOFTWARE
ASN A:389 , HOH A:5795
BINDING SITE FOR RESIDUE NAG A 3891
15
BC6
SOFTWARE
GLU A:388 , ASN A:420 , THR A:422 , ASN A:444 , NAG A:4202
BINDING SITE FOR RESIDUE NAG A 4201
16
BC7
SOFTWARE
NAG A:4201 , HOH A:5816
BINDING SITE FOR RESIDUE NAG A 4202
17
BC8
SOFTWARE
ALA A:484 , ARG A:503 , ASN A:504 , ASP A:513 , HOH A:5805
BINDING SITE FOR RESIDUE NAG A 5041
18
BC9
SOFTWARE
ASN A:544
BINDING SITE FOR RESIDUE NAG A 5441
19
CC1
SOFTWARE
ASN A:579 , ASN A:580 , THR A:581 , NAG A:5792
BINDING SITE FOR RESIDUE NAG A 5791
20
CC2
SOFTWARE
NAG A:5791 , HOH A:5817
BINDING SITE FOR RESIDUE NAG A 5792
[
close Site info
]
SAPs(SNPs)/Variants
(4, 4)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_019293 (R74Q, chain A, )
2: VAR_019294 (P242R, chain A, )
3: VAR_072435 (G404D, chain A, )
4: VAR_019295 (R497K, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_019293
R
98
Q
EGFR_HUMAN
Polymorphism
17289589
A
R
74
Q
2
UniProt
VAR_019294
P
266
R
EGFR_HUMAN
Polymorphism
17336639
A
P
242
R
3
UniProt
VAR_072435
G
428
D
EGFR_HUMAN
Disease (NISBD2)
---
A
G
404
D
4
UniProt
VAR_019295
R
521
K
EGFR_HUMAN
Polymorphism
2227983
A
R
497
K
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
(16, 16)
Info
All Exons
Exon 1.1e (A:2-6)
Exon 1.5 (A:6-56)
Exon 1.6 (A:57-118)
Exon 1.7b (A:118-163)
Exon 1.8 (A:163-186)
Exon 1.9 (A:186-225)
Exon 1.10 (A:226-273)
Exon 1.11 (A:273-312)
Exon 1.12 (A:312-354)
Exon 1.13a (A:354-379)
Exon 1.14 (A:379-409)
Exon 1.15 (A:409-476)
Exon 1.16 (A:476-520)
Exon 1.17 (A:520-550)
Exon 1.18 (A:551-603)
Exon 1.21 (A:603-614)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1e
02: Boundary 1.1e/1.5
03: Boundary 1.5/1.6
04: Boundary 1.6/1.7b
05: Boundary 1.7b/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 1.12/1.13a
11: Boundary 1.13a/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 1.18/1.21
17: Boundary 1.21/1.23
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
1.1e
ENST00000275493
1e
ENSE00001841347
chr7:
55086794-55087058
265
EGFR_HUMAN
1-30
30
1
A:2-6
5
1.5
ENST00000275493
5
ENSE00001715021
chr7:
55209979-55210130
152
EGFR_HUMAN
30-80
51
1
A:6-56
51
1.6
ENST00000275493
6
ENSE00001704157
chr7:
55210998-55211181
184
EGFR_HUMAN
81-142
62
1
A:57-118
62
1.7b
ENST00000275493
7b
ENSE00001798125
chr7:
55214299-55214433
135
EGFR_HUMAN
142-187
46
1
A:118-163
46
1.8
ENST00000275493
8
ENSE00001683983
chr7:
55218987-55219055
69
EGFR_HUMAN
187-210
24
1
A:163-186
24
1.9
ENST00000275493
9
ENSE00001652975
chr7:
55220239-55220357
119
EGFR_HUMAN
210-249
40
1
A:186-225
40
1.10
ENST00000275493
10
ENSE00001623732
chr7:
55221704-55221845
142
EGFR_HUMAN
250-297
48
1
A:226-273
48
1.11
ENST00000275493
11
ENSE00001751179
chr7:
55223523-55223639
117
EGFR_HUMAN
297-336
40
1
A:273-312
40
1.12
ENST00000275493
12
ENSE00001084929
chr7:
55224226-55224352
127
EGFR_HUMAN
336-378
43
1
A:312-354
43
1.13a
ENST00000275493
13a
ENSE00001084931
chr7:
55224452-55224525
74
EGFR_HUMAN
378-403
26
1
A:354-379
26
1.14
ENST00000275493
14
ENSE00001084926
chr7:
55225356-55225446
91
EGFR_HUMAN
403-433
31
1
A:379-409
31
1.15
ENST00000275493
15
ENSE00001084941
chr7:
55227832-55228031
200
EGFR_HUMAN
433-500
68
1
A:409-476
68
1.16
ENST00000275493
16
ENSE00001084939
chr7:
55229192-55229324
133
EGFR_HUMAN
500-544
45
1
A:476-520
45
1.17
ENST00000275493
17
ENSE00001084927
chr7:
55231426-55231516
91
EGFR_HUMAN
544-574
31
1
A:520-550
31
1.18
ENST00000275493
18
ENSE00001627115
chr7:
55232973-55233130
158
EGFR_HUMAN
575-627
53
1
A:551-603
53
1.21
ENST00000275493
21
ENSE00001768076
chr7:
55238868-55238906
39
EGFR_HUMAN
627-640
14
1
A:603-614
12
1.23
ENST00000275493
23
ENSE00001699330
chr7:
55240676-55240817
142
EGFR_HUMAN
640-687
48
0
-
-
1.24
ENST00000275493
24
ENSE00001778519
chr7:
55241614-55241736
123
EGFR_HUMAN
688-728
41
0
-
-
1.25
ENST00000275493
25
ENSE00001756460
chr7:
55242415-55242513
99
EGFR_HUMAN
729-761
33
0
-
-
1.26
ENST00000275493
26
ENSE00001601336
chr7:
55248986-55249171
186
EGFR_HUMAN
762-823
62
0
-
-
1.27
ENST00000275493
27
ENSE00001681524
chr7:
55259412-55259567
156
EGFR_HUMAN
824-875
52
0
-
-
1.28a
ENST00000275493
28a
ENSE00001631695
chr7:
55260459-55260534
76
EGFR_HUMAN
876-901
26
0
-
-
1.29
ENST00000275493
29
ENSE00001779947
chr7:
55266410-55266556
147
EGFR_HUMAN
901-950
50
0
-
-
1.30a
ENST00000275493
30a
ENSE00001790701
chr7:
55268009-55268106
98
EGFR_HUMAN
950-982
33
0
-
-
1.31
ENST00000275493
31
ENSE00001801208
chr7:
55268881-55269048
168
EGFR_HUMAN
983-1038
56
0
-
-
1.32
ENST00000275493
32
ENSE00001773562
chr7:
55269428-55269475
48
EGFR_HUMAN
1039-1054
16
0
-
-
1.33a
ENST00000275493
33a
ENSE00001795780
chr7:
55270210-55270318
109
EGFR_HUMAN
1055-1091
37
0
-
-
1.34b
ENST00000275493
34b
ENSE00001245887
chr7:
55272949-55279321
6373
EGFR_HUMAN
1091-1210
120
0
-
-
[
close EXON info
]
SCOP Domains
(3, 6)
Info
All SCOP Domains
1a: SCOP_d1yy9c1 (C:1-107)
1b: SCOP_d1yy9c2 (C:108-211)
2a: SCOP_d1yy9a1 (A:2-162)
2b: SCOP_d1yy9a2 (A:312-480)
3a: SCOP_d1yy9a3 (A:163-311)
3b: SCOP_d1yy9a4 (A:481-512)
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
:
automated matches
(864)
Protein domain
:
automated matches
(864)
Mouse (Mus musculus) [TaxId: 10090]
(360)
1a
d1yy9c1
C:1-107
1b
d1yy9c2
C:108-211
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
:
EGF receptor extracellular domain
(7)
Human (Homo sapiens) [TaxId: 9606]
(7)
2a
d1yy9a1
A:2-162
2b
d1yy9a2
A:312-480
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
:
EGF receptor Cys-rich domains
(6)
Human (Homo sapiens) [TaxId: 9606]
(6)
3a
d1yy9a3
A:163-311
3b
d1yy9a4
A:481-512
[
close SCOP info
]
CATH Domains
(3, 8)
Info
all CATH domains
1a: CATH_1yy9A01 (A:2-197)
1b: CATH_1yy9A03 (A:309-480)
2a: CATH_1yy9A02 (A:198-308)
2b: CATH_1yy9A04 (A:481-614)
3a: CATH_1yy9C02 (C:109-211)
3b: CATH_1yy9D02 (D:122-219)
3c: CATH_1yy9D01 (D:1-118)
3d: CATH_1yy9C01 (C: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
1yy9A01
A:2-197
1b
1yy9A03
A:309-480
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
1yy9A02
A:198-308
2b
1yy9A04
A:481-614
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
3a
1yy9C02
C:109-211
3b
1yy9D02
D:122-219
3c
1yy9D01
D:1-118
3d
1yy9C01
C:1-108
[
close CATH info
]
Pfam Domains
(2, 3)
Info
all PFAM domains
1a: PFAM_Furin_like_1yy9A01 (A:153-314)
2a: PFAM_Recep_L_domain_1yy9A02 (A:337-457)
2b: PFAM_Recep_L_domain_1yy9A03 (A:337-457)
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-1yy9A01
A:153-314
Clan
:
no clan defined [family: Recep_L_domain]
(12)
Family
:
Recep_L_domain
(12)
Homo sapiens (Human)
(9)
2a
Recep_L_domain-1yy9A02
A:337-457
2b
Recep_L_domain-1yy9A03
A:337-457
[
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 C
Chain D
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 (174 KB)
Header - Asym.Unit
Biol.Unit 1 (166 KB)
Header - Biol.Unit 1
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
1YY9
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help