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1Q9L
Biol. Unit 3
Info
Asym.Unit (154 KB)
Biol.Unit 1 (77 KB)
Biol.Unit 2 (76 KB)
Biol.Unit 3 (148 KB)
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(1)
Title
:
S25-2 FAB UNLIGANDED 2
Authors
:
H. P. Nguyen, N. O. Seto, C. R. Mackenzie, L. Brade, P. Kosma, H. Brade, S. V. Evans
Date
:
25 Aug 03 (Deposition) - 27 Jan 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.28
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-Carbohydrate, Anti-Lps, Antibody, Immunoglobulin, 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
)
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Hetero Components
(0, 0)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
1c: MAGNESIUM ION (MGc)
1d: MAGNESIUM ION (MGd)
1e: MAGNESIUM ION (MGe)
1f: MAGNESIUM ION (MGf)
1g: MAGNESIUM ION (MGg)
2a: ZINC ION (ZNa)
2b: ZINC ION (ZNb)
2c: ZINC ION (ZNc)
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Sites
(10, 10)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:184 , HIS A:188 , HOH A:690 , HOH A:702
BINDING SITE FOR RESIDUE ZN A 214
02
AC2
SOFTWARE
GLU C:184 , HIS C:188 , HOH C:674 , HOH C:688
BINDING SITE FOR RESIDUE ZN C 214
03
AC3
SOFTWARE
ASP C:1
BINDING SITE FOR RESIDUE ZN C 215
04
AC4
SOFTWARE
THR A:96 , PHE A:97 , TRP B:47 , HOH B:362
BINDING SITE FOR RESIDUE MG B 212
05
AC5
SOFTWARE
THR C:96 , PHE C:97 , TRP D:47 , HOH D:504
BINDING SITE FOR RESIDUE MG C 216
06
AC6
SOFTWARE
LYS C:89 , ARG C:95 , HOH C:631 , ASP D:95
BINDING SITE FOR RESIDUE MG C 217
07
AC7
SOFTWARE
ASP A:166 , LYS A:168 , HOH A:694 , HOH A:701 , HIS B:162 , HOH B:303 , HOH B:695
BINDING SITE FOR RESIDUE MG A 215
08
AC8
SOFTWARE
ASP C:166 , LYS C:168 , HOH C:314 , HIS D:162 , HOH D:351
BINDING SITE FOR RESIDUE MG C 218
09
AC9
SOFTWARE
GLU B:1 , HOH B:530 , ASP D:171
BINDING SITE FOR RESIDUE MG D 212
10
BC1
SOFTWARE
LYS C:148 , ASP C:150 , GLY C:151 , SER C:190 , THR C:192
BINDING SITE FOR RESIDUE MG C 219
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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PROSITE Patterns/Profiles
(, 0)
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Exons
(0, 0)
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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_d1q9lb2 (B:112-211)
1b: SCOP_d1q9ld2 (D:112-211)
2a: SCOP_d1q9la2 (A:108-213)
2b: SCOP_d1q9lc2 (C:108-213)
3a: SCOP_d1q9lb1 (B:1-111)
3b: SCOP_d1q9ld1 (D:1-111)
4a: SCOP_d1q9la1 (A:1-107)
4b: SCOP_d1q9lc1 (C:1-107)
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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)
Mouse (Mus musculus) [TaxId: 10090]
(414)
1a
d1q9lb2
B:112-211
1b
d1q9ld2
D:112-211
Protein domain
:
Immunoglobulin light chain kappa constant domain, CL-kappa
(495)
Mouse (Mus musculus) [TaxId: 10090]
(345)
2a
d1q9la2
A:108-213
2b
d1q9lc2
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
d1q9lb1
B:1-111
3b
d1q9ld1
D:1-111
Protein domain
:
Immunoglobulin light chain kappa variable domain, VL-kappa
(616)
Mouse (Mus musculus), cluster 1.2 [TaxId: 10090]
(46)
4a
d1q9la1
A:1-107
4b
d1q9lc1
C:1-107
[
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CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_1q9lA02 (A:108-210)
1b: CATH_1q9lB02 (B:112-210)
1c: CATH_1q9lD02 (D:112-210)
1d: CATH_1q9lA01 (A:1-107)
1e: CATH_1q9lC01 (C:1-107)
1f: CATH_1q9lB01 (B:1-111)
1g: CATH_1q9lD01 (D:1-111)
1h: CATH_1q9lC02 (C:108-210)
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Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
House mouse (Mus musculus)
(616)
1a
1q9lA02
A:108-210
1b
1q9lB02
B:112-210
1c
1q9lD02
D:112-210
1d
1q9lA01
A:1-107
1e
1q9lC01
C:1-107
1f
1q9lB01
B:1-111
1g
1q9lD01
D:1-111
1h
1q9lC02
C:108-210
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Pfam Domains
(0, 0)
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Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Asymmetric Unit 1
Asymmetric Unit 2
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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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Show PDB file:
Asym.Unit (154 KB)
Header - Asym.Unit
Biol.Unit 1 (77 KB)
Header - Biol.Unit 1
Biol.Unit 2 (76 KB)
Header - Biol.Unit 2
Biol.Unit 3 (148 KB)
Header - Biol.Unit 3
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