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3B2U
Biol. Unit 4
Info
Asym.Unit (794 KB)
Biol.Unit 1 (111 KB)
Biol.Unit 2 (110 KB)
Biol.Unit 3 (110 KB)
Biol.Unit 4 (113 KB)
Biol.Unit 5 (113 KB)
Biol.Unit 6 (112 KB)
Biol.Unit 7 (111 KB)
Biol.Unit 8 (112 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF ISOLATED DOMAIN III OF THE EXTRACELLULAR REGION OF THE EPIDERMAL GROWTH FACTOR RECEPTOR IN COMPLEX WITH THE FAB FRAGMENT OF IMC-11F8
Authors
:
K. M. Ferguson, S. Li, P. Kussie
Date
:
19 Oct 07 (Deposition) - 19 Feb 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.58
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X
Biol. Unit 1: A,H,L (1x)
Biol. Unit 2: B,C,D (1x)
Biol. Unit 3: E,F,G (1x)
Biol. Unit 4: I,J,K (1x)
Biol. Unit 5: M,N,O (1x)
Biol. Unit 6: P,Q,R (1x)
Biol. Unit 7: S,T,U (1x)
Biol. Unit 8: V,W,X (1x)
Keywords
:
Cell Surface Receptor; Glycoprotein; Antigen:Antibody Complex; Fab Fragment; Antitumor; Drug, Anti-Oncogene, Atp-Binding, Cell Cycle, Disease Mutation, Kinase, Membrane, Nucleotide-Binding, Phosphoprotein, Secreted, Transferase, Transmembrane, Tyrosine- Protein Kinase, Immune System-Transferase Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Li, P. Kussie, K. M. Ferguson
Structural Basis For Egf Receptor Inhibition By The Therapeutic Antibody Imc-11F8.
Structure V. 16 216 2008
[
close entry info
]
Hetero Components
(4, 11)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
1c: BETA-D-MANNOSE (BMAc)
1d: BETA-D-MANNOSE (BMAd)
1e: BETA-D-MANNOSE (BMAe)
1f: BETA-D-MANNOSE (BMAf)
1g: BETA-D-MANNOSE (BMAg)
1h: BETA-D-MANNOSE (BMAh)
1i: BETA-D-MANNOSE (BMAi)
1j: BETA-D-MANNOSE (BMAj)
1k: BETA-D-MANNOSE (BMAk)
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)
3a: N-ACETYL-D-GLUCOSAMINE (NAGa)
3aa: N-ACETYL-D-GLUCOSAMINE (NAGaa)
3ab: N-ACETYL-D-GLUCOSAMINE (NAGab)
3ac: N-ACETYL-D-GLUCOSAMINE (NAGac)
3ad: N-ACETYL-D-GLUCOSAMINE (NAGad)
3ae: N-ACETYL-D-GLUCOSAMINE (NAGae)
3af: N-ACETYL-D-GLUCOSAMINE (NAGaf)
3ag: N-ACETYL-D-GLUCOSAMINE (NAGag)
3ah: N-ACETYL-D-GLUCOSAMINE (NAGah)
3ai: N-ACETYL-D-GLUCOSAMINE (NAGai)
3aj: N-ACETYL-D-GLUCOSAMINE (NAGaj)
3ak: N-ACETYL-D-GLUCOSAMINE (NAGak)
3al: N-ACETYL-D-GLUCOSAMINE (NAGal)
3am: N-ACETYL-D-GLUCOSAMINE (NAGam)
3an: N-ACETYL-D-GLUCOSAMINE (NAGan)
3ao: N-ACETYL-D-GLUCOSAMINE (NAGao)
3ap: N-ACETYL-D-GLUCOSAMINE (NAGap)
3aq: N-ACETYL-D-GLUCOSAMINE (NAGaq)
3ar: N-ACETYL-D-GLUCOSAMINE (NAGar)
3as: N-ACETYL-D-GLUCOSAMINE (NAGas)
3at: N-ACETYL-D-GLUCOSAMINE (NAGat)
3au: N-ACETYL-D-GLUCOSAMINE (NAGau)
3av: N-ACETYL-D-GLUCOSAMINE (NAGav)
3aw: N-ACETYL-D-GLUCOSAMINE (NAGaw)
3ax: N-ACETYL-D-GLUCOSAMINE (NAGax)
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)
3l: N-ACETYL-D-GLUCOSAMINE (NAGl)
3m: N-ACETYL-D-GLUCOSAMINE (NAGm)
3n: N-ACETYL-D-GLUCOSAMINE (NAGn)
3o: N-ACETYL-D-GLUCOSAMINE (NAGo)
3p: N-ACETYL-D-GLUCOSAMINE (NAGp)
3q: N-ACETYL-D-GLUCOSAMINE (NAGq)
3r: N-ACETYL-D-GLUCOSAMINE (NAGr)
3s: N-ACETYL-D-GLUCOSAMINE (NAGs)
3t: N-ACETYL-D-GLUCOSAMINE (NAGt)
3u: N-ACETYL-D-GLUCOSAMINE (NAGu)
3v: N-ACETYL-D-GLUCOSAMINE (NAGv)
3w: N-ACETYL-D-GLUCOSAMINE (NAGw)
3x: N-ACETYL-D-GLUCOSAMINE (NAGx)
3y: N-ACETYL-D-GLUCOSAMINE (NAGy)
3z: N-ACETYL-D-GLUCOSAMINE (NAGz)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
4e: SULFATE ION (SO4e)
4f: SULFATE ION (SO4f)
4g: SULFATE ION (SO4g)
4h: SULFATE ION (SO4h)
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
7
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
4
SO4
1
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(11, 11)
Info
All Sites
01: AD3 (SOFTWARE)
02: AD4 (SOFTWARE)
03: AD5 (SOFTWARE)
04: CC6 (SOFTWARE)
05: CC7 (SOFTWARE)
06: DC1 (SOFTWARE)
07: DC2 (SOFTWARE)
08: DC3 (SOFTWARE)
09: DC4 (SOFTWARE)
10: DC5 (SOFTWARE)
11: HC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AD3
SOFTWARE
ASP I:323 , NAG I:3282 , MAN I:3284
BINDING SITE FOR RESIDUE BMA I 3283
02
AD4
SOFTWARE
ASP I:323 , BMA I:3283
BINDING SITE FOR RESIDUE MAN I 3284
03
AD5
SOFTWARE
NAG I:4201
BINDING SITE FOR RESIDUE NAG I 4202
04
CC6
SOFTWARE
SER I:324 , LEU I:325 , SER I:326 , ASN I:328 , ASN I:331 , THR I:358 , THR I:360 , NAG I:3282
BINDING SITE FOR RESIDUE NAG I 3281
05
CC7
SOFTWARE
NAG I:3281 , BMA I:3283 , HOH I:4237
BINDING SITE FOR RESIDUE NAG I 3282
06
DC1
SOFTWARE
ASN I:337
BINDING SITE FOR RESIDUE NAG I 3371
07
DC2
SOFTWARE
SER H:76 , ASN I:389 , NAG I:3892 , HOH I:4204 , HOH I:4242
BINDING SITE FOR RESIDUE NAG I 3891
08
DC3
SOFTWARE
THR H:75 , NAG I:3891 , BMA I:3893
BINDING SITE FOR RESIDUE NAG I 3892
09
DC4
SOFTWARE
SER H:28 , NAG I:3892 , HOH I:4233
BINDING SITE FOR RESIDUE BMA I 3893
10
DC5
SOFTWARE
GLU I:388 , ASN I:389 , ASN I:420 , ASN I:444 , NAG I:4202 , HOH I:4210
BINDING SITE FOR RESIDUE NAG I 4201
11
HC7
SOFTWARE
LYS K:190 , ARG K:211
BINDING SITE FOR RESIDUE SO4 K 214
[
close Site info
]
SAPs(SNPs)/Variants
(4, 4)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_066403 (W148R, chain K, )
2: VAR_003897 (V191L, chain K, )
3: VAR_072435 (G404D, chain I, )
4: VAR_019295 (R497K, chain I, )
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)
---
K
W
148
R
2
UniProt
VAR_003897
V
83
L
IGKC_HUMAN
Unclassified
---
K
V
191
L
3
UniProt
VAR_072435
G
428
D
EGFR_HUMAN
Disease (NISBD2)
---
I
G
404
D
4
UniProt
VAR_019295
R
521
K
EGFR_HUMAN
Polymorphism
2227983
I
R
497
K
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: IG_MHC (K:192-198)
;
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
1
-
-
K:192-198
-
-
-
-
-
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(5, 48)
Info
All SCOP Domains
1a: SCOP_d3b2ud1 (D:1-107)
1b: SCOP_d3b2ud2 (D:108-213)
1c: SCOP_d3b2ug1 (G:1-107)
1d: SCOP_d3b2ug2 (G:108-213)
1e: SCOP_d3b2uk1 (K:1-107)
1f: SCOP_d3b2uk2 (K:108-213)
1g: SCOP_d3b2ul1 (L:1-107)
1h: SCOP_d3b2ul2 (L:108-213)
1i: SCOP_d3b2uo1 (O:1-107)
1j: SCOP_d3b2uo2 (O:108-213)
1k: SCOP_d3b2ur1 (R:1-107)
1l: SCOP_d3b2ur2 (R:108-213)
1m: SCOP_d3b2uu1 (U:1-107)
1n: SCOP_d3b2uu2 (U:108-213)
1o: SCOP_d3b2ux1 (X:1-107)
1p: SCOP_d3b2ux2 (X:108-213)
2a: SCOP_d3b2uc2 (C:122-221)
2b: SCOP_d3b2uf2 (F:122-221)
2c: SCOP_d3b2uh2 (H:122-221)
2d: SCOP_d3b2uj2 (J:122-221)
2e: SCOP_d3b2un2 (N:122-221)
2f: SCOP_d3b2uq2 (Q:122-221)
2g: SCOP_d3b2ut2 (T:122-221)
2h: SCOP_d3b2uw2 (W:122-221)
3a: SCOP_d3b2uc1 (C:1-121)
3b: SCOP_d3b2uf1 (F:1-121)
3c: SCOP_d3b2uh1 (H:1-121)
3d: SCOP_d3b2uj1 (J:1-121)
3e: SCOP_d3b2un1 (N:1-121)
3f: SCOP_d3b2uq1 (Q:1-121)
3g: SCOP_d3b2ut1 (T:1-121)
3h: SCOP_d3b2uw1 (W:1-121)
4a: SCOP_d3b2ua1 (A:308-480)
4b: SCOP_d3b2ub1 (B:309-480)
4c: SCOP_d3b2ue1 (E:309-480)
4d: SCOP_d3b2ui1 (I:310-480)
4e: SCOP_d3b2um1 (M:308-480)
4f: SCOP_d3b2up1 (P:310-480)
4g: SCOP_d3b2us1 (S:309-480)
4h: SCOP_d3b2uv1 (V:310-480)
5a: SCOP_d3b2ua2 (A:481-502)
5b: SCOP_d3b2ub2 (B:481-502)
5c: SCOP_d3b2ue2 (E:481-502)
5d: SCOP_d3b2ui2 (I:481-502)
5e: SCOP_d3b2um2 (M:481-502)
5f: SCOP_d3b2up2 (P:481-502)
5g: SCOP_d3b2us2 (S:481-502)
5h: SCOP_d3b2uv2 (V:481-502)
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)
Human (Homo sapiens) [TaxId: 9606]
(448)
1a
d3b2ud1
D:1-107
1b
d3b2ud2
D:108-213
1c
d3b2ug1
G:1-107
1d
d3b2ug2
G:108-213
1e
d3b2uk1
K:1-107
1f
d3b2uk2
K:108-213
1g
d3b2ul1
L:1-107
1h
d3b2ul2
L:108-213
1i
d3b2uo1
O:1-107
1j
d3b2uo2
O:108-213
1k
d3b2ur1
R:1-107
1l
d3b2ur2
R:108-213
1m
d3b2uu1
U:1-107
1n
d3b2uu2
U:108-213
1o
d3b2ux1
X:1-107
1p
d3b2ux2
X:108-213
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)
2a
d3b2uc2
C:122-221
2b
d3b2uf2
F:122-221
2c
d3b2uh2
H:122-221
2d
d3b2uj2
J:122-221
2e
d3b2un2
N:122-221
2f
d3b2uq2
Q:122-221
2g
d3b2ut2
T:122-221
2h
d3b2uw2
W:122-221
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)
3a
d3b2uc1
C:1-121
3b
d3b2uf1
F:1-121
3c
d3b2uh1
H:1-121
3d
d3b2uj1
J:1-121
3e
d3b2un1
N:1-121
3f
d3b2uq1
Q:1-121
3g
d3b2ut1
T:1-121
3h
d3b2uw1
W:1-121
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)
4a
d3b2ua1
A:308-480
4b
d3b2ub1
B:309-480
4c
d3b2ue1
E:309-480
4d
d3b2ui1
I:310-480
4e
d3b2um1
M:308-480
4f
d3b2up1
P:310-480
4g
d3b2us1
S:309-480
4h
d3b2uv1
V:310-480
Class
:
Small proteins
(3458)
Fold
:
Knottins (small inhibitors, toxins, lectins)
(761)
Superfamily
:
Growth factor receptor domain
(25)
Family
:
automated matches
(7)
Protein domain
:
automated matches
(7)
Human (Homo sapiens) [TaxId: 9606]
(7)
5a
d3b2ua2
A:481-502
5b
d3b2ub2
B:481-502
5c
d3b2ue2
E:481-502
5d
d3b2ui2
I:481-502
5e
d3b2um2
M:481-502
5f
d3b2up2
P:481-502
5g
d3b2us2
S:481-502
5h
d3b2uv2
V:481-502
[
close SCOP info
]
CATH Domains
(2, 40)
Info
all CATH domains
1a: CATH_3b2uI00 (I:310-502)
1b: CATH_3b2uP00 (P:310-502)
1c: CATH_3b2uV00 (V:310-502)
1d: CATH_3b2uB00 (B:309-502)
1e: CATH_3b2uE00 (E:309-502)
1f: CATH_3b2uS00 (S:309-502)
1g: CATH_3b2uA00 (A:308-502)
1h: CATH_3b2uM00 (M:308-502)
2a: CATH_3b2uD02 (D:109-211)
2b: CATH_3b2uD01 (D:1-108)
2c: CATH_3b2uG01 (G:1-108)
2d: CATH_3b2uK01 (K:1-108)
2e: CATH_3b2uL01 (L:1-108)
2f: CATH_3b2uO01 (O:1-108)
2g: CATH_3b2uR01 (R:1-108)
2h: CATH_3b2uU01 (U:1-108)
2i: CATH_3b2uX01 (X:1-108)
2j: CATH_3b2uH02 (H:122-219)
2k: CATH_3b2uJ02 (J:122-219)
2l: CATH_3b2uN02 (N:122-219)
2m: CATH_3b2uQ02 (Q:122-219)
2n: CATH_3b2uF02 (F:122-219)
2o: CATH_3b2uT02 (T:122-219)
2p: CATH_3b2uW02 (W:122-219)
2q: CATH_3b2uC02 (C:122-219)
2r: CATH_3b2uC01 (C:1-121)
2s: CATH_3b2uF01 (F:1-121)
2t: CATH_3b2uH01 (H:1-121)
2u: CATH_3b2uJ01 (J:1-121)
2v: CATH_3b2uN01 (N:1-121)
2w: CATH_3b2uQ01 (Q:1-121)
2x: CATH_3b2uT01 (T:1-121)
2y: CATH_3b2uW01 (W:1-121)
2z: CATH_3b2uG02 (G:109-211)
2aa: CATH_3b2uK02 (K:109-211)
2ab: CATH_3b2uL02 (L:109-211)
2ac: CATH_3b2uO02 (O:109-211)
2ad: CATH_3b2uR02 (R:109-211)
2ae: CATH_3b2uU02 (U:109-211)
2af: CATH_3b2uX02 (X:109-211)
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
3b2uI00
I:310-502
1b
3b2uP00
P:310-502
1c
3b2uV00
V:310-502
1d
3b2uB00
B:309-502
1e
3b2uE00
E:309-502
1f
3b2uS00
S:309-502
1g
3b2uA00
A:308-502
1h
3b2uM00
M:308-502
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Human (Homo sapiens)
(912)
2a
3b2uD02
D:109-211
2b
3b2uD01
D:1-108
2c
3b2uG01
G:1-108
2d
3b2uK01
K:1-108
2e
3b2uL01
L:1-108
2f
3b2uO01
O:1-108
2g
3b2uR01
R:1-108
2h
3b2uU01
U:1-108
2i
3b2uX01
X:1-108
2j
3b2uH02
H:122-219
2k
3b2uJ02
J:122-219
2l
3b2uN02
N:122-219
2m
3b2uQ02
Q:122-219
2n
3b2uF02
F:122-219
2o
3b2uT02
T:122-219
2p
3b2uW02
W:122-219
2q
3b2uC02
C:122-219
2r
3b2uC01
C:1-121
2s
3b2uF01
F:1-121
2t
3b2uH01
H:1-121
2u
3b2uJ01
J:1-121
2v
3b2uN01
N:1-121
2w
3b2uQ01
Q:1-121
2x
3b2uT01
T:1-121
2y
3b2uW01
W:1-121
2z
3b2uG02
G:109-211
2aa
3b2uK02
K:109-211
2ab
3b2uL02
L:109-211
2ac
3b2uO02
O:109-211
2ad
3b2uR02
R:109-211
2ae
3b2uU02
U:109-211
2af
3b2uX02
X:109-211
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