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Getting 'Biological Unit' information from database.
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Getting 'Hetero Component' information from database.
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4BSV
Asym. Unit
Info
Asym.Unit (168 KB)
Biol.Unit 1 (156 KB)
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(1)
Title
:
HETERODIMERIC FC ANTIBODY AZYMETRIC VARIANT 1
Authors
:
M. D. L. Suits, T. Spreter, E. E. Cabrera, S. B. Dixit, P. I. Lario, D. K. Y. I. E. P. D'Angelo, M. J. Boulanger
Date
:
11 Jun 13 (Deposition) - 21 Aug 13 (Release) - 23 Apr 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.75
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Immune System, Antibody, Bispecific, Scaffold, Antibody Engineering, Zymeworks Inc.
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. S. Von Kreudenstein, E. Escobar-Carbrera, P. I. Lario, I. D'Angelo, K. Brault, J. Kelly, Y. Durocher, J. Baardsnes, R. J. Woods, M. H. Xie, P. Girod, M. D. L. Suits, M. J. Boulanger, D. K. Y. Poon, G. Y. K. Ng, S. B. Dixit
Improving Biophysical Properties Of A Bispecific Antibody Scaffold To Aid Developability: Quality By Molecular Design
Mabs V. 5 646 2013
[
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Hetero Components
(7, 30)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
2f: 1,2-ETHANEDIOL (EDOf)
2g: 1,2-ETHANEDIOL (EDOg)
2h: 1,2-ETHANEDIOL (EDOh)
2i: 1,2-ETHANEDIOL (EDOi)
3a: ALPHA-L-FUCOSE (FUCa)
3b: ALPHA-L-FUCOSE (FUCb)
4a: BETA-D-GALACTOSE (GALa)
4b: BETA-D-GALACTOSE (GALb)
5a: IODIDE ION (IODa)
5b: IODIDE ION (IODb)
5c: IODIDE ION (IODc)
6a: ALPHA-D-MANNOSE (MANa)
6b: ALPHA-D-MANNOSE (MANb)
6c: ALPHA-D-MANNOSE (MANc)
6d: ALPHA-D-MANNOSE (MANd)
7a: N-ACETYL-D-GLUCOSAMINE (NAGa)
7b: N-ACETYL-D-GLUCOSAMINE (NAGb)
7c: N-ACETYL-D-GLUCOSAMINE (NAGc)
7d: N-ACETYL-D-GLUCOSAMINE (NAGd)
7e: N-ACETYL-D-GLUCOSAMINE (NAGe)
7f: N-ACETYL-D-GLUCOSAMINE (NAGf)
7g: N-ACETYL-D-GLUCOSAMINE (NAGg)
7h: N-ACETYL-D-GLUCOSAMINE (NAGh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
2
Ligand/Ion
BETA-D-MANNOSE
2
EDO
9
Ligand/Ion
1,2-ETHANEDIOL
3
FUC
2
Ligand/Ion
ALPHA-L-FUCOSE
4
GAL
2
Ligand/Ion
BETA-D-GALACTOSE
5
IOD
3
Ligand/Ion
IODIDE ION
6
MAN
4
Ligand/Ion
ALPHA-D-MANNOSE
7
NAG
8
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(16, 16)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
MET A:252 , MET A:428 , LYS B:248 , SER B:254 , ARG B:255 , HOH B:2009 , HOH B:2229
BINDING SITE FOR RESIDUE EDO B1455
02
AC2
SOFTWARE
ILE A:377 , ALA A:378 , VAL A:379 , HOH A:2126 , EDO B:1457 , HOH B:2170 , HOH B:2233 , HOH B:2234 , HOH B:4122
BINDING SITE FOR RESIDUE EDO A1455
03
AC3
SOFTWARE
GLN A:362 , HOH A:4089 , LYS B:370 , ASP B:399 , SER B:400 , ASP B:401 , EDO B:1459 , HOH B:2140
BINDING SITE FOR RESIDUE EDO A1461
04
AC4
SOFTWARE
SER A:324 , ASN A:325 , LYS A:326
BINDING SITE FOR RESIDUE EDO A1462
05
AC5
SOFTWARE
ALA B:378 , VAL B:379 , HOH B:2179 , HOH B:2230 , HOH B:2231 , HOH B:4113
BINDING SITE FOR RESIDUE EDO B1456
06
AC6
SOFTWARE
ALA A:378 , VAL A:379 , EDO A:1455 , HOH A:2126 , HOH A:2147 , GLY B:385 , HOH B:2170 , HOH B:2233 , HOH B:2234 , HOH B:4122
BINDING SITE FOR RESIDUE EDO B1457
07
AC7
SOFTWARE
PHE A:243 , NAG A:1451 , HOH A:4004
BINDING SITE FOR RESIDUE EDO A1456
08
AC8
SOFTWARE
PRO B:247 , SER B:375 , ASP B:376 , ILE B:377 , HOH B:2151 , HOH B:2153 , HOH B:2230 , HOH B:4112
BINDING SITE FOR RESIDUE EDO B1458
09
AC9
SOFTWARE
GLN A:362 , LYS A:409 , THR A:411 , EDO A:1461 , LYS B:370 , ASP B:399 , HOH B:2140 , HOH B:4139
BINDING SITE FOR RESIDUE EDO B1459
10
BC1
SOFTWARE
SER B:254
BINDING SITE FOR RESIDUE IOD B1460
11
BC2
SOFTWARE
SER B:254
BINDING SITE FOR RESIDUE IOD B1461
12
BC3
SOFTWARE
ASP A:265 , GLN A:295 , ASN A:297 , NAG A:1448 , HOH A:2021 , HOH A:4017 , HOH A:4035
BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A1446 THROUGH FUC A1447 BOUND TO ASN A 297
13
BC4
SOFTWARE
ASN A:384 , PRO B:244 , PRO B:245 , LYS B:246 , GLU B:258 , THR B:260 , VAL B:264 , ASP B:265 , GLU B:272 , GLN B:295 , TYR B:296 , ASN B:297 , ARG B:301 , MAN B:1453 , HOH B:2004 , HOH B:2057 , HOH B:2223 , HOH B:2224 , HOH B:2226 , HOH B:2228 , HOH B:4051 , HOH B:4052 , HOH B:4175
BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG B1446 THROUGH GAL B1452 BOUND TO ASN B 297
14
BC5
SOFTWARE
PHE A:241 , PHE A:243 , PRO A:244 , LYS A:246 , GLU A:258 , THR A:260 , VAL A:262 , VAL A:264 , ARG A:301 , NAG A:1446 , FUC A:1447 , MAN A:1453 , EDO A:1456 , HOH A:2006 , HOH A:2043 , HOH A:2180 , HOH A:2182 , HOH A:2183 , HOH A:2184 , HOH A:2185 , HOH A:2186 , HOH A:4004 , HOH A:4007 , HOH A:4017 , HOH A:4036 , HOH A:4152 , HOH A:4154 , HOH A:4156 , ASN B:384 , VAL B:422 , HOH B:2164 , HOH B:2167 , HOH B:2168 , HOH B:2195 , HOH B:2200 , HOH B:4120
BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A1448 THROUGH GAL A1452
15
BC6
SOFTWARE
PHE A:241 , PHE A:243 , PRO A:244 , LYS A:246 , GLU A:258 , THR A:260 , NAG A:1448 , EDO A:1456 , HOH A:2006 , HOH A:2043 , HOH A:2182 , HOH A:2183 , HOH A:2184 , HOH A:2185 , HOH A:2186 , HOH A:4004 , HOH A:4007 , HOH A:4036 , HOH A:4154 , HOH A:4156 , ASN B:384 , VAL B:422 , HOH B:2164 , HOH B:2167 , HOH B:2168 , HOH B:2195 , HOH B:2200 , HOH B:4120
BINDING SITE FOR POLY-SACCHARIDE RESIDUES MAN A1453 THROUGH NAG A1454
16
BC7
SOFTWARE
BMA B:1449
BINDING SITE FOR POLY-SACCHARIDE RESIDUES MAN B1453 THROUGH NAG B1454
[
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]
SAPs(SNPs)/Variants
(2, 4)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_003887 (D356E, chain A/B, )
2: VAR_003888 (L358M, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_003887
D
239
E
IGHG1_HUMAN
Unclassified
---
A/B
D
356
E
2
UniProt
VAR_003888
L
241
M
IGHG1_HUMAN
Unclassified
---
A/B
L
358
M
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: IG_MHC (-|A:423-429,B:423-429)
;
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.
IGHG1_HUMAN
81-87
306-312
2
-
A:423-429
B:423-429
[
close PROSITE info
]
Exons
(2, 4)
Info
All Exons
Exon 1.3b (A:236-341 | B:236-341)
Exon 1.4c (A:341-445 | B:341-445)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.2/1.3b
2: Boundary 1.3b/1.4c
3: Boundary 1.4c/-
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
1.1
ENST00000390549
1
ENSE00001838294
chr14:
106209408-106209114
295
IGHG1_HUMAN
1-99
99
0
-
-
1.2
ENST00000390549
2
ENSE00001719055
chr14:
106208722-106208678
45
IGHG1_HUMAN
99-114
16
0
-
-
1.3b
ENST00000390549
3b
ENSE00001776617
chr14:
106208559-106208230
330
IGHG1_HUMAN
114-224
111
2
A:236-341
B:236-341
106
106
1.4c
ENST00000390549
4c
ENSE00001837466
chr14:
106208132-106207675
458
IGHG1_HUMAN
224-330
107
2
A:341-445
B:341-445
111
111
[
close EXON info
]
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d4bsva1 (A:236-341)
1b: SCOP_d4bsva2 (A:342-445)
1c: SCOP_d4bsvb1 (B:236-341)
1d: SCOP_d4bsvb2 (B:342-445)
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Classes
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(
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(
)
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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
:
automated matches
(864)
Protein domain
:
automated matches
(864)
Human (Homo sapiens) [TaxId: 9606]
(448)
1a
d4bsva1
A:236-341
1b
d4bsva2
A:342-445
1c
d4bsvb1
B:236-341
1d
d4bsvb2
B:342-445
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
[
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]
Atom Selection
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)
Protein
Nucleic
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Hetero
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All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
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Chain B
Asymmetric Unit 1
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select residue range 5 to 10 in chain 'A'
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Asym.Unit (168 KB)
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