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3C09
Biol. Unit 1
Info
Asym.Unit (181 KB)
Biol.Unit 1 (93 KB)
Biol.Unit 2 (85 KB)
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(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
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Hetero Components
(2, 5)
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
1
Ligand/Ion
BETA-D-MANNOSE
2
MAN
-1
Ligand/Ion
ALPHA-D-MANNOSE
3
NAG
4
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
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Sites
(4, 4)
Info
All Sites
1: AC5 (SOFTWARE)
2: AC6 (SOFTWARE)
3: AC7 (SOFTWARE)
4: AC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
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
2
AC6
SOFTWARE
ASP D:323
BINDING SITE FOR RESIDUE NAG D 3282
3
AC7
SOFTWARE
ASP D:323
BINDING SITE FOR RESIDUE BMA D 3283
4
AC8
SOFTWARE
LYS D:336 , ASN D:337
BINDING SITE FOR RESIDUE NAG D 3371
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SAPs(SNPs)/Variants
(4, 4)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_066403 (W147R, chain L, )
2: VAR_003897 (V190L, chain L, )
3: VAR_072435 (G404D, chain D, )
4: VAR_019295 (R497K, chain D, )
View:
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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)
---
D
G
404
D
4
UniProt
VAR_019295
R
521
K
EGFR_HUMAN
Polymorphism
2227983
D
R
497
K
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: IG_MHC (L:191-197)
;
View:
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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
-
L:191-197
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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
(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)
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Classes
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)
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)
Folds
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)
(
)
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)
(
)
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)
(
)
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
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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)
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Topologies
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)
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
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Atom Selection
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Protein
Nucleic
Backbone
Sidechain
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Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain D
Chain H
Chain L
Asymmetric Unit 1
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Asym.Unit (181 KB)
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