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3N85
Biol. Unit 1
Info
Asym.Unit (359 KB)
Biol.Unit 1, α-C (1.0 MB)
Biol.Unit 1 (1.0 MB)
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(1)
Title
:
CRYSTALLOGRAPHIC TRIMER OF HER2 EXTRACELLULAR REGIONS IN COMPLEX WITH TRYPTOPHAN-RICH ANTIBODY FRAGMENT
Authors
:
C. Eigenbrot
Date
:
27 May 10 (Deposition) - 28 Jul 10 (Release) - 15 Jan 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.20
Chains
:
Asym. Unit : A,H,L
Biol. Unit 1: A,H,L (3x)
Keywords
:
Her2, Erbb2, Trp/Ser Library, Phage Display, Transferase-Immune System Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. D. Fisher, M. Ultsch, A. Lingel, G. Schaefer, L. Shao, S. Birtalan, S. S. Sidhu, C. Eigenbrot
Structure Of The Complex Between Her2 And An Antibody Paratope Formed By Side Chains From Tryptophan And Serine.
J. Mol. Biol. V. 402 217 2010
[
close entry info
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Hetero Components
(4, 69)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
2a: CHLORIDE ION (CLa)
3a: ALPHA-L-FUCOSE (FUCa)
4a: N-ACETYL-D-GLUCOSAMINE (NAGa)
4b: N-ACETYL-D-GLUCOSAMINE (NAGb)
4c: N-ACETYL-D-GLUCOSAMINE (NAGc)
4d: N-ACETYL-D-GLUCOSAMINE (NAGd)
5a: SULFATE ION (SO4a)
5b: SULFATE ION (SO4b)
5c: SULFATE ION (SO4c)
5d: SULFATE ION (SO4d)
5e: SULFATE ION (SO4e)
5f: SULFATE ION (SO4f)
5g: SULFATE ION (SO4g)
5h: SULFATE ION (SO4h)
5i: SULFATE ION (SO4i)
5j: SULFATE ION (SO4j)
5k: SULFATE ION (SO4k)
5l: SULFATE ION (SO4l)
5m: SULFATE ION (SO4m)
5n: SULFATE ION (SO4n)
5o: SULFATE ION (SO4o)
5p: SULFATE ION (SO4p)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
6
Ligand/Ion
BETA-D-MANNOSE
2
CL
-1
Ligand/Ion
CHLORIDE ION
3
FUC
3
Ligand/Ion
ALPHA-L-FUCOSE
4
NAG
12
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
5
SO4
48
Ligand/Ion
SULFATE ION
[
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Sites
(24, 24)
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)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR A:45 , VAL A:69 , ARG A:70
BINDING SITE FOR RESIDUE CL A 625
02
AC2
SOFTWARE
PRO A:372 , PRO A:394 , ASP A:395 , SER A:396 , TRP H:96
BINDING SITE FOR RESIDUE SO4 A 626
03
AC3
SOFTWARE
HIS A:456 , HIS A:473 , THR A:474 , ALA A:475 , ASN A:476
BINDING SITE FOR RESIDUE SO4 A 627
04
AC4
SOFTWARE
LYS A:128 , GLN A:217 , GLU A:243 , LEU A:244
BINDING SITE FOR RESIDUE SO4 A 628
05
AC5
SOFTWARE
ALA A:15 , TYR A:389 , ASN A:416
BINDING SITE FOR RESIDUE SO4 A 629
06
AC6
SOFTWARE
ARG A:514 , ARG A:523 , SER H:82B
BINDING SITE FOR RESIDUE SO4 A 630
07
AC7
SOFTWARE
GLU A:373 , SER H:25 , GLY H:26 , PHE H:27 , ASN H:76
BINDING SITE FOR RESIDUE SO4 H 225
08
AC8
SOFTWARE
VAL A:575 , ALA A:576 , ARG A:577
BINDING SITE FOR RESIDUE SO4 A 631
09
AC9
SOFTWARE
SER L:30 , ARG L:66
BINDING SITE FOR RESIDUE SO4 L 218
10
BC1
SOFTWARE
LYS A:148 , ASN A:154 , GLY A:200
BINDING SITE FOR RESIDUE SO4 A 632
11
BC2
SOFTWARE
GLN A:462 , ARG A:495 , HIS A:497 , VAL A:507 , ASN A:508
BINDING SITE FOR RESIDUE SO4 A 633
12
BC3
SOFTWARE
PRO L:59 , SER L:60
BINDING SITE FOR RESIDUE SO4 L 219
13
BC4
SOFTWARE
ARG A:410 , ARG A:437 , GLU A:438
BINDING SITE FOR RESIDUE SO4 A 634
14
BC5
SOFTWARE
GLU A:485 , GLY A:486 , TRP H:56
BINDING SITE FOR RESIDUE SO4 A 635
15
BC6
SOFTWARE
MET A:9 , PRO A:14 , ALA A:15 , SER A:16 , HIS A:20 , MET A:23 , TYR A:419
BINDING SITE FOR RESIDUE SO4 A 636
16
BC7
SOFTWARE
HIS A:152 , LYS A:153
BINDING SITE FOR RESIDUE SO4 A 637
17
BC8
SOFTWARE
SER A:16 , GLU A:18 , HIS A:447 , HIS A:448 , THR A:474
BINDING SITE FOR RESIDUE SO4 A 638
18
BC9
SOFTWARE
GLN A:134 , ASP A:163 , ASN A:165 , ALA A:169 , CYS A:170 , PRO A:172 , NAG A:1166 , FUC A:1170
BINDING SITE FOR RESIDUE NAG A 1165
19
CC1
SOFTWARE
HIS A:171 , PRO A:172 , NAG A:1165 , BMA A:1167 , FUC A:1170
BINDING SITE FOR RESIDUE NAG A 1166
20
CC2
SOFTWARE
NAG A:1166
BINDING SITE FOR RESIDUE BMA A 1167
21
CC3
SOFTWARE
NAG A:1165 , NAG A:1166
BINDING SITE FOR RESIDUE FUC A 1170
22
CC4
SOFTWARE
CYS A:230 , ASN A:237 , SER A:239 , NAG A:1238
BINDING SITE FOR RESIDUE NAG A 1237
23
CC5
SOFTWARE
NAG A:1237 , BMA A:1239
BINDING SITE FOR RESIDUE NAG A 1238
24
CC6
SOFTWARE
NAG A:1238
BINDING SITE FOR RESIDUE BMA A 1239
[
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SAPs(SNPs)/Variants
(1, 3)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_016317 (W430C, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_016317
W
452
C
ERBB2_HUMAN
Polymorphism
4252633
A
W
430
C
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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End label:
Sorry, no Info available
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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
(0, 0)
Info
All SCOP Domains
View:
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Label:
Sorry, no Info available
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CATH Domains
(0, 0)
Info
all CATH domains
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Label:
Sorry, no Info available
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Pfam Domains
(2, 3)
Info
all PFAM domains
1a: PFAM_Furin_like_3n85A01 (A:161-321)
2a: PFAM_Recep_L_domain_3n85A02 (A:344-464)
2b: PFAM_Recep_L_domain_3n85A03 (A:344-464)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: Furin-like]
(12)
Family
:
Furin-like
(12)
Homo sapiens (Human)
(9)
1a
Furin-like-3n85A01
A:161-321
Clan
:
no clan defined [family: Recep_L_domain]
(12)
Family
:
Recep_L_domain
(12)
Homo sapiens (Human)
(9)
2a
Recep_L_domain-3n85A02
A:344-464
2b
Recep_L_domain-3n85A03
A:344-464
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Atom Selection
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)
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Nucleic
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Sidechain
Hetero
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Solvent
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Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain H
Chain L
Asymmetric Unit 1
Asymmetric Unit 2
Asymmetric Unit 3
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Example Command
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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)
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Note:
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View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
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Asym.Unit (359 KB)
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