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.
3C09
Asym. Unit
Info
Asym.Unit (181 KB)
Biol.Unit 1 (93 KB)
Biol.Unit 2 (85 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE THE FAB FRAGMENT OF MATUZUMAB (FAB72000) IN COMPLEX WITH DOMAIN III OF THE EXTRACELLULAR REGION OF EGFR
Authors
:
K. M. Ferguson, J. Schmiedel, T. Knoechel
Date
:
18 Jan 08 (Deposition) - 15 Apr 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.20
Chains
:
Asym. Unit : A,B,C,D,H,L
Biol. Unit 1: D,H,L (1x)
Biol. Unit 2: A,B,C (1x)
Keywords
:
Cell Surface Receptor, Glycoprotein, Antigen, Antibody Complex, Fab Fragment, Antitumor, Drug Immune System-Transferase Complex, Immune System-Transferase Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Schmiedel, A. Blaukat, S. Li, T. Knochel, K. M. Ferguson
Matuzumab Binding To Egfr Prevents The Conformational Rearrangement Required For Dimerization.
Cancer Cell V. 13 365 2008
[
close entry info
]
Hetero Components
(3, 13)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
2a: ALPHA-D-MANNOSE (MANa)
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)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
2
Ligand/Ion
BETA-D-MANNOSE
2
MAN
1
Ligand/Ion
ALPHA-D-MANNOSE
3
NAG
10
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:323 , SER A:324 , LEU A:325 , SER A:326 , ASN A:328 , ASN A:331 , THR A:358 , THR A:360
BINDING SITE FOR RESIDUE NAG A 3281
2
AC2
SOFTWARE
ASP A:323
BINDING SITE FOR RESIDUE NAG A 3282
3
AC3
SOFTWARE
ASP A:323
BINDING SITE FOR RESIDUE BMA A 3283
4
AC4
SOFTWARE
GLU A:388 , ASN A:420 , ASN A:444
BINDING SITE FOR RESIDUE NAG A 4201
5
AC5
SOFTWARE
ASP D:323 , SER D:326 , ASN D:328 , ASN D:331 , THR D:358 , THR D:360
BINDING SITE FOR RESIDUE NAG D 3281
6
AC6
SOFTWARE
ASP D:323
BINDING SITE FOR RESIDUE NAG D 3282
7
AC7
SOFTWARE
ASP D:323
BINDING SITE FOR RESIDUE BMA D 3283
8
AC8
SOFTWARE
LYS D:336 , ASN D:337
BINDING SITE FOR RESIDUE NAG D 3371
[
close Site info
]
SAPs(SNPs)/Variants
(4, 6)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_066403 (W147R, chain L, )
2: VAR_003897 (V190L, chain L, )
3: VAR_072435 (G404D, chain A/D, )
4: VAR_019295 (R497K, chain A/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_066403
W
40
R
IGKC_HUMAN
Disease (IGKCD)
---
L
W
147
R
2
UniProt
VAR_003897
V
83
L
IGKC_HUMAN
Unclassified
---
L
V
190
L
3
UniProt
VAR_072435
G
428
D
EGFR_HUMAN
Disease (NISBD2)
---
A/D
G
404
D
4
UniProt
VAR_019295
R
521
K
EGFR_HUMAN
Polymorphism
2227983
A/D
R
497
K
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: IG_MHC (B:195-197,L:191-197)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
IG_MHC
PS00290
Immunoglobulins and major histocompatibility complex proteins signature.
IGKC_HUMAN
85-91
2
B:195-197
L:191-197
[
close PROSITE info
]
Exons
(6, 12)
Info
All Exons
Exon 1.11 (A:310-312 | D:310-312)
Exon 1.12 (A:312-354 | D:312-354)
Exon 1.13a (A:354-379 | D:354-379)
Exon 1.14 (A:379-409 | D:379-409)
Exon 1.15 (A:409-476 | D:409-476)
Exon 1.16 (A:476-500 | D:476-500)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.10/1.11
2: Boundary 1.11/1.12
3: Boundary 1.12/1.13a
4: Boundary 1.13a/1.14
5: Boundary 1.14/1.15
6: Boundary 1.15/1.16
7: Boundary 1.16/1.17
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
0
-
-
1.5
ENST00000275493
5
ENSE00001715021
chr7:
55209979-55210130
152
EGFR_HUMAN
30-80
51
0
-
-
1.6
ENST00000275493
6
ENSE00001704157
chr7:
55210998-55211181
184
EGFR_HUMAN
81-142
62
0
-
-
1.7b
ENST00000275493
7b
ENSE00001798125
chr7:
55214299-55214433
135
EGFR_HUMAN
142-187
46
0
-
-
1.8
ENST00000275493
8
ENSE00001683983
chr7:
55218987-55219055
69
EGFR_HUMAN
187-210
24
0
-
-
1.9
ENST00000275493
9
ENSE00001652975
chr7:
55220239-55220357
119
EGFR_HUMAN
210-249
40
0
-
-
1.10
ENST00000275493
10
ENSE00001623732
chr7:
55221704-55221845
142
EGFR_HUMAN
250-297
48
0
-
-
1.11
ENST00000275493
11
ENSE00001751179
chr7:
55223523-55223639
117
EGFR_HUMAN
297-336
40
2
A:310-312
D:310-312
3
3
1.12
ENST00000275493
12
ENSE00001084929
chr7:
55224226-55224352
127
EGFR_HUMAN
336-378
43
2
A:312-354
D:312-354
43
43
1.13a
ENST00000275493
13a
ENSE00001084931
chr7:
55224452-55224525
74
EGFR_HUMAN
378-403
26
2
A:354-379
D:354-379
26
26
1.14
ENST00000275493
14
ENSE00001084926
chr7:
55225356-55225446
91
EGFR_HUMAN
403-433
31
2
A:379-409
D:379-409
31
31
1.15
ENST00000275493
15
ENSE00001084941
chr7:
55227832-55228031
200
EGFR_HUMAN
433-500
68
2
A:409-476
D:409-476
68
68
1.16
ENST00000275493
16
ENSE00001084939
chr7:
55229192-55229324
133
EGFR_HUMAN
500-544
45
2
A:476-500
D:476-500
25
25
1.17
ENST00000275493
17
ENSE00001084927
chr7:
55231426-55231516
91
EGFR_HUMAN
544-574
31
0
-
-
1.18
ENST00000275493
18
ENSE00001627115
chr7:
55232973-55233130
158
EGFR_HUMAN
575-627
53
0
-
-
1.21
ENST00000275493
21
ENSE00001768076
chr7:
55238868-55238906
39
EGFR_HUMAN
627-640
14
0
-
-
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
(4, 8)
Info
All SCOP Domains
1a: SCOP_d3c09c2 (C:122-218)
1b: SCOP_d3c09h2 (H:122-218)
2a: SCOP_d3c09c1 (C:2-121)
2b: SCOP_d3c09h1 (H:2-121)
3a: SCOP_d3c09a1 (A:312-480)
3b: SCOP_d3c09d1 (D:312-480)
4a: SCOP_d3c09a2 (A:481-500)
4b: SCOP_d3c09d2 (D:481-500)
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
d3c09c2
C:122-218
1b
d3c09h2
H:122-218
Family
:
V set domains (antibody variable domain-like)
(1919)
Protein domain
:
Immunoglobulin heavy chain variable domain, VH
(658)
Human (Homo sapiens), cluster 3 [TaxId: 9606]
(33)
2a
d3c09c1
C:2-121
2b
d3c09h1
H:2-121
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)
3a
d3c09a1
A:312-480
3b
d3c09d1
D: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)
4a
d3c09a2
A:481-500
4b
d3c09d2
D:481-500
[
close SCOP info
]
CATH Domains
(2, 10)
Info
all CATH domains
1a: CATH_3c09A00 (A:310-500)
1b: CATH_3c09D00 (D:310-500)
2a: CATH_3c09L02 (L:108-211)
2b: CATH_3c09B01 (B:1-107)
2c: CATH_3c09L01 (L:1-107)
2d: CATH_3c09H02 (H:118-222)
2e: CATH_3c09C02 (C:118-218)
2f: CATH_3c09C01 (C:1-117)
2g: CATH_3c09H01 (H:1-117)
2h: CATH_3c09B02 (B:108-206)
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, house mouse (Homo sapiens, mus musculus)
(1)
1a
3c09A00
A:310-500
1b
3c09D00
D:310-500
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human, house mouse (Homo sapiens, mus musculus)
(6)
2a
3c09L02
L:108-211
2b
3c09B01
B:1-107
2c
3c09L01
L:1-107
2d
3c09H02
H:118-222
2e
3c09C02
C:118-218
2f
3c09C01
C:1-117
2g
3c09H01
H:1-117
2h
3c09B02
B:108-206
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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 H
Chain L
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 (181 KB)
Header - Asym.Unit
Biol.Unit 1 (93 KB)
Header - Biol.Unit 1
Biol.Unit 2 (85 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
3C09
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help