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1Q9W
Asym. Unit
Info
Asym.Unit (165 KB)
Biol.Unit 1 (82 KB)
Biol.Unit 2 (81 KB)
Biol.Unit 3 (158 KB)
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(1)
Title
:
S45-18 FAB PENTASACCHARIDE BISPHOSPHATE COMPLEX
Authors
:
H. P. Nguyen, N. O. Seto, C. R. Mackenzie, L. Brade, P. Kosma, H. Brade, S. V. Evans
Date
:
26 Aug 03 (Deposition) - 27 Jan 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.75
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Biol. Unit 3: A,B,C,D (1x)
Keywords
:
Antigen-Binding Fragment, Fab, Anti-Cabohydrate, Anti-Lps, Antibody, Immunoglobulin, Kdo, Protein-Carbohydrate Complex, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. P. Nguyen, N. O. Seto, C. R. Mackenzie, L. Brade, P. Kosma, H. Brade, S. V. Evans
Germline Antibody Recognition Of Distinct Carbohydrate Epitopes.
Nat. Struct. Biol. V. 10 1019 2003
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(4, 13)
Info
All Hetero Components
1a: GLUCOSAMINE 1-PHOSPHATE (GP1a)
2a: GLUCOSAMINE 4-PHOSPHATE (GP4a)
3a: 3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACI... (KDOa)
3b: 3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACI... (KDOb)
3c: 3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACI... (KDOc)
3d: 3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACI... (KDOd)
3e: 3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACI... (KDOe)
3f: 3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACI... (KDOf)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
4c: MAGNESIUM ION (MGc)
4d: MAGNESIUM ION (MGd)
4e: MAGNESIUM ION (MGe)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GP1
1
Ligand/Ion
GLUCOSAMINE 1-PHOSPHATE
2
GP4
1
Ligand/Ion
GLUCOSAMINE 4-PHOSPHATE
3
KDO
6
Ligand/Ion
3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID
4
MG
5
Ligand/Ion
MAGNESIUM ION
[
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]
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
ASN A:30A , ARG A:30C , PRO B:14 , PHE B:97 , KDO B:302 , GP4 B:304 , GP1 B:305 , HOH B:340 , HOH B:526
BINDING SITE FOR RESIDUE KDO B 301
02
AC2
SOFTWARE
TYR B:33 , LYS B:52D , PHE B:97 , KDO B:301 , KDO B:303 , GP1 B:305 , HOH B:309A , HOH B:310A , HOH B:320 , HOH B:340 , HOH B:354 , HOH B:361 , HOH B:475
BINDING SITE FOR RESIDUE KDO B 302
03
AC3
SOFTWARE
SER A:91 , TYR A:92 , ARG A:95 , HOH A:216A , TYR B:33 , ARG B:52 , ILE B:96 , KDO B:302 , HOH B:307A , HOH B:308A , HOH B:419 , HOH B:475
BINDING SITE FOR RESIDUE KDO B 303
04
AC4
SOFTWARE
SER B:111 , KDO B:301 , GP1 B:305 , HOH B:375 , HOH B:415
BINDING SITE FOR RESIDUE GP4 B 304
05
AC5
SOFTWARE
LYS B:52D , SER B:111 , KDO B:301 , KDO B:302 , GP4 B:304 , HOH B:320 , HOH B:344 , HOH B:361 , HOH B:439
BINDING SITE FOR RESIDUE GP1 B 305
06
AC6
SOFTWARE
ASN C:30A , ARG C:30C , KDO C:312 , KDO C:313 , PHE D:97
BINDING SITE FOR RESIDUE KDO C 311
07
AC7
SOFTWARE
HOH B:423 , KDO C:311 , KDO C:313 , HOH C:379 , TYR D:33 , LYS D:52D , PHE D:97 , HOH D:214B
BINDING SITE FOR RESIDUE KDO C 312
08
AC8
SOFTWARE
SER C:91 , TYR C:92 , ARG C:95 , KDO C:311 , KDO C:312 , HOH C:316B , HOH C:317B , HOH C:318B , HOH C:378 , TYR D:33 , ARG D:52 , ILE D:96
BINDING SITE FOR RESIDUE KDO C 313
09
AC9
SOFTWARE
GLU B:56 , HOH B:376 , HOH B:377 , HOH B:378 , HOH B:379 , GLU D:56
BINDING SITE FOR RESIDUE MG B 306
10
BC1
SOFTWARE
PHE A:97 , GLU B:46 , TRP B:47 , HOH B:312
BINDING SITE FOR RESIDUE MG A 214
11
BC2
SOFTWARE
THR C:96 , PHE C:97 , HOH C:397 , GLU D:46 , TRP D:47 , HOH D:344
BINDING SITE FOR RESIDUE MG C 314
12
BC3
SOFTWARE
GLN A:6 , MET A:21 , SER A:22 , TRP A:35 , THR A:101
BINDING SITE FOR RESIDUE MG A 215
13
BC4
SOFTWARE
GLN C:6 , MET C:21 , SER C:22 , THR C:101
BINDING SITE FOR RESIDUE MG C 315
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
[
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: IG_MHC (A:191-197,C:191-197)
;
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_MOUSE
84-90
2
A:191-197
C:191-197
[
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]
Exons
(0, 0)
Info
All Exons
View:
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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.
SCOP Domains
(4, 8)
Info
All SCOP Domains
1a: SCOP_d1q9wb2 (B:112-213)
1b: SCOP_d1q9wd2 (D:112-213)
2a: SCOP_d1q9wa2 (A:108-213)
2b: SCOP_d1q9wc2 (C:108-213)
3a: SCOP_d1q9wb1 (B:1-111)
3b: SCOP_d1q9wd1 (D:1-111)
4a: SCOP_d1q9wa1 (A:1-107)
4b: SCOP_d1q9wc1 (C:1-107)
View:
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(
)
(
)
Folds
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(
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)
(
)
Families
(
)
(
)
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)
Mouse (Mus musculus) [TaxId: 10090]
(414)
1a
d1q9wb2
B:112-213
1b
d1q9wd2
D:112-213
Protein domain
:
Immunoglobulin light chain kappa constant domain, CL-kappa
(495)
Mouse (Mus musculus) [TaxId: 10090]
(345)
2a
d1q9wa2
A:108-213
2b
d1q9wc2
C:108-213
Family
:
V set domains (antibody variable domain-like)
(1919)
Protein domain
:
Immunoglobulin heavy chain variable domain, VH
(658)
Mouse (Mus musculus), cluster 1 [TaxId: 10090]
(57)
3a
d1q9wb1
B:1-111
3b
d1q9wd1
D:1-111
Protein domain
:
Immunoglobulin light chain kappa variable domain, VL-kappa
(616)
Mouse (Mus musculus), cluster 1.2 [TaxId: 10090]
(46)
4a
d1q9wa1
A:1-107
4b
d1q9wc1
C:1-107
[
close SCOP info
]
CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_1q9wA02 (A:108-210)
1b: CATH_1q9wB02 (B:112-210)
1c: CATH_1q9wD02 (D:112-209)
1d: CATH_1q9wC02 (C:108-210)
1e: CATH_1q9wA01 (A:1-107)
1f: CATH_1q9wC01 (C:1-107)
1g: CATH_1q9wB01 (B:1-111)
1h: CATH_1q9wD01 (D:1-111)
View:
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)
(
)
Architectures
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)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
House mouse (Mus musculus)
(616)
1a
1q9wA02
A:108-210
1b
1q9wB02
B:112-210
1c
1q9wD02
D:112-209
1d
1q9wC02
C:108-210
1e
1q9wA01
A:1-107
1f
1q9wC01
C:1-107
1g
1q9wB01
B:1-111
1h
1q9wD01
D:1-111
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Sorry, no Info available
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Atom Selection
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Chain D
Asymmetric Unit 1
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select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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Asym.Unit (165 KB)
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