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.
1NQL
Asym. Unit
Info
Asym.Unit (112 KB)
Biol.Unit 1 (105 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 HUMAN EPIDERMAL GROWTH FACTOR (EGF) RECEPTOR IN AN INACTIVE (LOW PH) COMPLEX WITH EGF.
Authors
:
K. M. Ferguson, M. A. Lemmon
Date
:
21 Jan 03 (Deposition) - 11 Mar 03 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Cell Surface Receptor, Tyrosine Kinase, Glycoprotein, Endosomal, Growth Factor, Auto-Inhibition, Hormone-Growth Factor Receptor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. M. Ferguson, M. B. Berger, J. M. Mendrola, H. Cho, D. J. Leahy, M. A. Lemmon
Egf Activates Its Receptor By Removing Interactions That Auto-Inhibit Ectodomain Dimerization
Mol. Cell V. 11 507 2003
[
close entry info
]
Hetero Components
(2, 13)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
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)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
2
Ligand/Ion
BETA-D-MANNOSE
2
NAG
11
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
GLN A:28 , ASN A:32 , ASN A:33
BINDING SITE FOR RESIDUE NAG A 625
02
AC2
SOFTWARE
SER A:324 , LEU A:325 , SER A:326 , ASN A:328 , ASN A:331 , THR A:358 , NAG A:3282
BINDING SITE FOR RESIDUE NAG A 3281
03
AC3
SOFTWARE
ASP A:323 , NAG A:3281 , BMA A:3283
BINDING SITE FOR RESIDUE NAG A 3282
04
AC4
SOFTWARE
ASP A:323 , NAG A:3282
BINDING SITE FOR RESIDUE BMA A 3283
05
AC5
SOFTWARE
ASN A:337 , NAG A:3372
BINDING SITE FOR RESIDUE NAG A 3371
06
AC6
SOFTWARE
NAG A:3371 , BMA A:3373
BINDING SITE FOR RESIDUE NAG A 3372
07
AC7
SOFTWARE
NAG A:3372
BINDING SITE FOR RESIDUE BMA A 3373
08
AC8
SOFTWARE
GLU A:388 , ASN A:389 , ASN A:420 , ASN A:444 , NAG A:4202
BINDING SITE FOR RESIDUE NAG A 4201
09
AC9
SOFTWARE
NAG A:4201
BINDING SITE FOR RESIDUE NAG A 4202
10
BC1
SOFTWARE
ARG A:503 , ASN A:504 , ASP A:513
BINDING SITE FOR RESIDUE NAG A 5041
11
BC2
SOFTWARE
TYR A:101 , ALA A:542 , ASN A:544 , NAG A:5442 , GLU B:24 , ALA B:25
BINDING SITE FOR RESIDUE NAG A 5441
12
BC3
SOFTWARE
TYR A:101 , HIS A:594 , NAG A:5441 , ALA B:25
BINDING SITE FOR RESIDUE NAG A 5442
13
BC4
SOFTWARE
PRO A:241 , ASN A:256 , GLU A:258 , MET A:576 , GLY A:577 , ASN A:579
BINDING SITE FOR RESIDUE NAG A 5791
[
close Site info
]
SAPs(SNPs)/Variants
(5, 5)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_020971 (D11E, chain B, )
2: VAR_019293 (R74Q, chain A, )
3: VAR_019294 (P242R, chain A, )
4: VAR_072435 (G404D, chain A, )
5: VAR_019295 (R497K, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_020971
D
981
E
EGF_HUMAN
Polymorphism
11569086
B
D
11
E
2
UniProt
VAR_019293
R
98
Q
EGFR_HUMAN
Polymorphism
17289589
A
R
74
Q
3
UniProt
VAR_019294
P
266
R
EGFR_HUMAN
Polymorphism
17336639
A
P
242
R
4
UniProt
VAR_072435
G
428
D
EGFR_HUMAN
Disease (NISBD2)
---
A
G
404
D
5
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
(2, 1)
Info
All PROSITE Patterns/Profiles
1: EGF_2 (-|-|-|-|-|-|B:31-42)
2: EGF_1 (B:31-42)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
EGF_2
PS01186
EGF-like domain signature 2.
EGF_HUMAN
339-354
380-395
461-476
765-780
855-868
897-910
1001-1012
1
-
-
-
-
-
-
B:31-42
2
EGF_1
PS00022
EGF-like domain signature 1.
EGF_HUMAN
1001-1012
1
B:31-42
[
close PROSITE info
]
Exons
(18, 18)
Info
All Exons
Exon 1.20 (B:3-32)
Exon 1.21 (B:32-50)
Exon 2.1e (A:3-6)
Exon 2.5 (A:6-56)
Exon 2.6 (A:57-118)
Exon 2.7b (A:118-163)
Exon 2.8 (A:163-186)
Exon 2.9 (A:186-225)
Exon 2.10 (A:226-273)
Exon 2.11 (A:273-312)
Exon 2.12 (A:312-354)
Exon 2.13a (A:354-379)
Exon 2.14 (A:379-409)
Exon 2.15 (A:409-476)
Exon 2.16 (A:476-520)
Exon 2.17 (A:520-550)
Exon 2.18 (A:551-603)
Exon 2.21 (A:603-614)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.19/1.20
02: Boundary 1.20/1.21
03: Boundary 1.21/1.22
04: Boundary -/2.1e
05: Boundary 2.1e/2.5
06: Boundary 2.5/2.6
07: Boundary 2.6/2.7b
08: Boundary 2.7b/2.8
09: Boundary 2.8/2.9
10: Boundary 2.9/2.10
11: Boundary 2.10/2.11
12: Boundary 2.11/2.12
13: Boundary 2.12/2.13a
14: Boundary 2.13a/2.14
15: Boundary 2.14/2.15
16: Boundary 2.15/2.16
17: Boundary 2.16/2.17
18: Boundary 2.17/2.18
19: Boundary 2.18/2.21
20: Boundary 2.21/2.23
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
1.1b
ENST00000265171
1b
ENSE00001081340
chr4:
110834047-110834618
572
EGF_HUMAN
1-43
43
0
-
-
1.2b
ENST00000265171
2b
ENSE00000736651
chr4:
110862102-110862301
200
EGF_HUMAN
43-109
67
0
-
-
1.3a
ENST00000265171
3a
ENSE00000736652
chr4:
110864410-110864591
182
EGF_HUMAN
110-170
61
0
-
-
1.4b
ENST00000265171
4b
ENSE00000736653
chr4:
110864998-110865225
228
EGF_HUMAN
170-246
77
0
-
-
1.5
ENST00000265171
5
ENSE00000736654
chr4:
110866229-110866431
203
EGF_HUMAN
246-314
69
0
-
-
1.6b
ENST00000265171
6b
ENSE00000736655
chr4:
110880468-110880593
126
EGF_HUMAN
314-356
43
0
-
-
1.7
ENST00000265171
7
ENSE00000736656
chr4:
110882023-110882145
123
EGF_HUMAN
356-397
42
0
-
-
1.8
ENST00000265171
8
ENSE00000736657
chr4:
110883019-110883141
123
EGF_HUMAN
397-438
42
0
-
-
1.9b
ENST00000265171
9b
ENSE00000736658
chr4:
110884329-110884454
126
EGF_HUMAN
438-480
43
0
-
-
1.10
ENST00000265171
10
ENSE00000736659
chr4:
110885557-110885693
137
EGF_HUMAN
480-525
46
0
-
-
1.11b
ENST00000265171
11b
ENSE00000736660
chr4:
110890127-110890275
149
EGF_HUMAN
526-575
50
0
-
-
1.12
ENST00000265171
12
ENSE00000736662
chr4:
110895859-110895963
105
EGF_HUMAN
575-610
36
0
-
-
1.13b
ENST00000265171
13b
ENSE00000736665
chr4:
110897168-110897391
224
EGF_HUMAN
610-685
76
0
-
-
1.14
ENST00000265171
14
ENSE00000736668
chr4:
110901128-110901295
168
EGF_HUMAN
685-741
57
0
-
-
1.15c
ENST00000265171
15c
ENSE00000736670
chr4:
110901982-110902131
150
EGF_HUMAN
741-791
51
0
-
-
1.16
ENST00000265171
16
ENSE00000736672
chr4:
110904578-110904697
120
EGF_HUMAN
791-831
41
0
-
-
1.17b
ENST00000265171
17b
ENSE00000736674
chr4:
110908900-110909016
117
EGF_HUMAN
831-870
40
0
-
-
1.18
ENST00000265171
18
ENSE00000736676
chr4:
110909740-110909865
126
EGF_HUMAN
870-912
43
0
-
-
1.19
ENST00000265171
19
ENSE00000736679
chr4:
110914403-110914525
123
EGF_HUMAN
912-953
42
0
-
-
1.20
ENST00000265171
20
ENSE00000736682
chr4:
110915889-110916036
148
EGF_HUMAN
953-1002
50
1
B:3-32
30
1.21
ENST00000265171
21
ENSE00000736686
chr4:
110920835-110921002
168
EGF_HUMAN
1002-1058
57
1
B:32-50
19
1.22
ENST00000265171
22
ENSE00000736691
chr4:
110925661-110925778
118
EGF_HUMAN
1058-1097
40
0
-
-
1.23
ENST00000265171
23
ENSE00000736696
chr4:
110929308-110929386
79
EGF_HUMAN
1098-1124
27
0
-
-
1.24d
ENST00000265171
24d
ENSE00001081339
chr4:
110932358-110933422
1065
EGF_HUMAN
1124-1207
84
0
-
-
2.1e
ENST00000275493
1e
ENSE00001841347
chr7:
55086794-55087058
265
EGFR_HUMAN
1-30
30
1
A:3-6
4
2.5
ENST00000275493
5
ENSE00001715021
chr7:
55209979-55210130
152
EGFR_HUMAN
30-80
51
1
A:6-56
51
2.6
ENST00000275493
6
ENSE00001704157
chr7:
55210998-55211181
184
EGFR_HUMAN
81-142
62
1
A:57-118
62
2.7b
ENST00000275493
7b
ENSE00001798125
chr7:
55214299-55214433
135
EGFR_HUMAN
142-187
46
1
A:118-163
46
2.8
ENST00000275493
8
ENSE00001683983
chr7:
55218987-55219055
69
EGFR_HUMAN
187-210
24
1
A:163-186
24
2.9
ENST00000275493
9
ENSE00001652975
chr7:
55220239-55220357
119
EGFR_HUMAN
210-249
40
1
A:186-225
40
2.10
ENST00000275493
10
ENSE00001623732
chr7:
55221704-55221845
142
EGFR_HUMAN
250-297
48
1
A:226-273
48
2.11
ENST00000275493
11
ENSE00001751179
chr7:
55223523-55223639
117
EGFR_HUMAN
297-336
40
1
A:273-312
40
2.12
ENST00000275493
12
ENSE00001084929
chr7:
55224226-55224352
127
EGFR_HUMAN
336-378
43
1
A:312-354
43
2.13a
ENST00000275493
13a
ENSE00001084931
chr7:
55224452-55224525
74
EGFR_HUMAN
378-403
26
1
A:354-379
26
2.14
ENST00000275493
14
ENSE00001084926
chr7:
55225356-55225446
91
EGFR_HUMAN
403-433
31
1
A:379-409
31
2.15
ENST00000275493
15
ENSE00001084941
chr7:
55227832-55228031
200
EGFR_HUMAN
433-500
68
1
A:409-476
68
2.16
ENST00000275493
16
ENSE00001084939
chr7:
55229192-55229324
133
EGFR_HUMAN
500-544
45
1
A:476-520
45
2.17
ENST00000275493
17
ENSE00001084927
chr7:
55231426-55231516
91
EGFR_HUMAN
544-574
31
1
A:520-550
31
2.18
ENST00000275493
18
ENSE00001627115
chr7:
55232973-55233130
158
EGFR_HUMAN
575-627
53
1
A:551-603
53
2.21
ENST00000275493
21
ENSE00001768076
chr7:
55238868-55238906
39
EGFR_HUMAN
627-640
14
1
A:603-614
12
2.23
ENST00000275493
23
ENSE00001699330
chr7:
55240676-55240817
142
EGFR_HUMAN
640-687
48
0
-
-
2.24
ENST00000275493
24
ENSE00001778519
chr7:
55241614-55241736
123
EGFR_HUMAN
688-728
41
0
-
-
2.25
ENST00000275493
25
ENSE00001756460
chr7:
55242415-55242513
99
EGFR_HUMAN
729-761
33
0
-
-
2.26
ENST00000275493
26
ENSE00001601336
chr7:
55248986-55249171
186
EGFR_HUMAN
762-823
62
0
-
-
2.27
ENST00000275493
27
ENSE00001681524
chr7:
55259412-55259567
156
EGFR_HUMAN
824-875
52
0
-
-
2.28a
ENST00000275493
28a
ENSE00001631695
chr7:
55260459-55260534
76
EGFR_HUMAN
876-901
26
0
-
-
2.29
ENST00000275493
29
ENSE00001779947
chr7:
55266410-55266556
147
EGFR_HUMAN
901-950
50
0
-
-
2.30a
ENST00000275493
30a
ENSE00001790701
chr7:
55268009-55268106
98
EGFR_HUMAN
950-982
33
0
-
-
2.31
ENST00000275493
31
ENSE00001801208
chr7:
55268881-55269048
168
EGFR_HUMAN
983-1038
56
0
-
-
2.32
ENST00000275493
32
ENSE00001773562
chr7:
55269428-55269475
48
EGFR_HUMAN
1039-1054
16
0
-
-
2.33a
ENST00000275493
33a
ENSE00001795780
chr7:
55270210-55270318
109
EGFR_HUMAN
1055-1091
37
0
-
-
2.34b
ENST00000275493
34b
ENSE00001245887
chr7:
55272949-55279321
6373
EGFR_HUMAN
1091-1210
120
0
-
-
[
close EXON info
]
SCOP Domains
(3, 5)
Info
All SCOP Domains
1a: SCOP_d1nqla1 (A:3-162)
1b: SCOP_d1nqla2 (A:312-480)
2a: SCOP_d1nqlb_ (B:)
3a: SCOP_d1nqla3 (A:163-311)
3b: SCOP_d1nqla4 (A:481-614)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
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)
1a
d1nqla1
A:3-162
1b
d1nqla2
A:312-480
Class
:
Small proteins
(3458)
Fold
:
Knottins (small inhibitors, toxins, lectins)
(761)
Superfamily
:
EGF/Laminin
(347)
Family
:
EGF-type module
(304)
Protein domain
:
Epidermal growth factor, EGF
(13)
Human (Homo sapiens) [TaxId: 9606]
(5)
2a
d1nqlb_
B:
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
d1nqla3
A:163-311
3b
d1nqla4
A:481-614
[
close SCOP info
]
CATH Domains
(3, 5)
Info
all CATH domains
1a: CATH_1nqlA01 (A:3-190)
1b: CATH_1nqlA03 (A:310-481)
2a: CATH_1nqlA02 (A:191-309)
2b: CATH_1nqlA04 (A:482-614)
3a: CATH_1nqlB00 (B:3-50)
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
1nqlA01
A:3-190
1b
1nqlA03
A:310-481
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
1nqlA02
A:191-309
2b
1nqlA04
A:482-614
Topology
:
Laminin
(270)
Homologous Superfamily
:
Laminin
(263)
Human (Homo sapiens)
(195)
3a
1nqlB00
B:3-50
[
close CATH info
]
Pfam Domains
(3, 4)
Info
all PFAM domains
1a: PFAM_EGF_1nqlB01 (B:6-41)
2a: PFAM_Furin_like_1nqlA01 (A:153-314)
3a: PFAM_Recep_L_domain_1nqlA02 (A:337-457)
3b: PFAM_Recep_L_domain_1nqlA03 (A:337-457)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
EGF
(60)
Family
:
EGF
(31)
Homo sapiens (Human)
(25)
1a
EGF-1nqlB01
B:6-41
Clan
:
no clan defined [family: Furin-like]
(12)
Family
:
Furin-like
(12)
Homo sapiens (Human)
(9)
2a
Furin-like-1nqlA01
A:153-314
Clan
:
no clan defined [family: Recep_L_domain]
(12)
Family
:
Recep_L_domain
(12)
Homo sapiens (Human)
(9)
3a
Recep_L_domain-1nqlA02
A:337-457
3b
Recep_L_domain-1nqlA03
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 B
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 (112 KB)
Header - Asym.Unit
Biol.Unit 1 (105 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
1NQL
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help