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3CFJ
Biol. Unit 1
Info
Asym.Unit (289 KB)
Biol.Unit 1 (75 KB)
Biol.Unit 2 (75 KB)
Biol.Unit 3 (74 KB)
Biol.Unit 4 (74 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF CATALYTIC ELIMINATION ANTIBODY 34E4, ORTHORHOMBIC CRYSTAL FORM
Authors
:
E. W. Debler, I. A. Wilson
Date
:
04 Mar 08 (Deposition) - 15 Apr 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B,C,D,E,F,H,L
Biol. Unit 1: H,L (1x)
Biol. Unit 2: A,B (1x)
Biol. Unit 3: C,D (1x)
Biol. Unit 4: E,F (1x)
Keywords
:
Immunoglobulin, Catalytic Antibody, Chimeric Fab, Apo Form, Proton Transfer, Conformational Change, Immune System, Immunoglobulin Domain, Immunoglobulin V Region
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. W. Debler, R. Muller, D. Hilvert, I. A. Wilson
Conformational Isomerism Can Limit Antibody Catalysis.
J. Biol. Chem. V. 283 16554 2008
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Hetero Components
(2, 2)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
1
Ligand/Ion
GLYCEROL
2
SO4
1
Ligand/Ion
SULFATE ION
[
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Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
LEU H:63 , LYS H:66 , ARG H:82B , ARG H:83
BINDING SITE FOR RESIDUE SO4 H 602
2
AC2
SOFTWARE
ARG D:55 , ILE H:57 , ASN H:58 , TYR H:59 , ASN L:94 , HIS L:95
BINDING SITE FOR RESIDUE SO4 D 601
3
AC4
SOFTWARE
PHE H:174 , PRO H:175 , LEU H:187 , SER H:188 , GLN L:160 , SER L:162 , SER L:176 , SER L:177 , THR L:178
BINDING SITE FOR RESIDUE GOL L 701
[
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SAPs(SNPs)/Variants
(2, 2)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_066403 (W148R, chain L, )
2: VAR_003897 (V191L, chain L, )
View:
Select:
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
148
R
2
UniProt
VAR_003897
V
83
L
IGKC_HUMAN
Unclassified
---
L
V
191
L
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:192-198)
;
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:192-198
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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, 16)
Info
All SCOP Domains
1a: SCOP_d3cfja1 (A:1-106)
1b: SCOP_d3cfjc1 (C:1-106)
1c: SCOP_d3cfje1 (E:1-106)
1d: SCOP_d3cfjl1 (L:1-106)
2a: SCOP_d3cfjb2 (B:114-228)
2b: SCOP_d3cfjd2 (D:114-228)
2c: SCOP_d3cfjf2 (F:114-228)
2d: SCOP_d3cfjh2 (H:114-228)
3a: SCOP_d3cfja2 (A:107-213)
3b: SCOP_d3cfjc2 (C:107-213)
3c: SCOP_d3cfje2 (E:107-213)
3d: SCOP_d3cfjl2 (L:107-213)
4a: SCOP_d3cfjb1 (B:1-113)
4b: SCOP_d3cfjd1 (D:1-113)
4c: SCOP_d3cfjf1 (F:1-113)
4d: SCOP_d3cfjh1 (H:1-113)
View:
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Classes
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)
(
)
Folds
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)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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)
Mouse (Mus musculus) [TaxId: 10090]
(360)
1a
d3cfja1
A:1-106
1b
d3cfjc1
C:1-106
1c
d3cfje1
E:1-106
1d
d3cfjl1
L:1-106
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)
2a
d3cfjb2
B:114-228
2b
d3cfjd2
D:114-228
2c
d3cfjf2
F:114-228
2d
d3cfjh2
H:114-228
Protein domain
:
Immunoglobulin light chain kappa constant domain, CL-kappa
(495)
Human (Homo sapiens) [TaxId: 9606]
(144)
3a
d3cfja2
A:107-213
3b
d3cfjc2
C:107-213
3c
d3cfje2
E:107-213
3d
d3cfjl2
L:107-213
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)
4a
d3cfjb1
B:1-113
4b
d3cfjd1
D:1-113
4c
d3cfjf1
F:1-113
4d
d3cfjh1
H:1-113
[
close SCOP info
]
CATH Domains
(1, 16)
Info
all CATH domains
1a: CATH_3cfjA02 (A:109-213)
1b: CATH_3cfjL02 (L:109-213)
1c: CATH_3cfjB02 (B:114-228)
1d: CATH_3cfjD02 (D:114-228)
1e: CATH_3cfjF02 (F:114-228)
1f: CATH_3cfjH02 (H:114-228)
1g: CATH_3cfjA01 (A:1-108)
1h: CATH_3cfjC01 (C:1-108)
1i: CATH_3cfjE01 (E:1-108)
1j: CATH_3cfjL01 (L:1-108)
1k: CATH_3cfjB01 (B:1-113)
1l: CATH_3cfjD01 (D:1-113)
1m: CATH_3cfjF01 (F:1-113)
1n: CATH_3cfjH01 (H:1-113)
1o: CATH_3cfjC02 (C:109-213)
1p: CATH_3cfjE02 (E:109-213)
View:
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)
(
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(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Mouse, human (Mus musculus, homo sapiens)
(6)
1a
3cfjA02
A:109-213
1b
3cfjL02
L:109-213
1c
3cfjB02
B:114-228
1d
3cfjD02
D:114-228
1e
3cfjF02
F:114-228
1f
3cfjH02
H:114-228
1g
3cfjA01
A:1-108
1h
3cfjC01
C:1-108
1i
3cfjE01
E:1-108
1j
3cfjL01
L:1-108
1k
3cfjB01
B:1-113
1l
3cfjD01
D:1-113
1m
3cfjF01
F:1-113
1n
3cfjH01
H:1-113
1o
3cfjC02
C:109-213
1p
3cfjE02
E:109-213
[
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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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Chain H
Chain L
Asymmetric Unit 1
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Show PDB file:
Asym.Unit (289 KB)
Header - Asym.Unit
Biol.Unit 1 (75 KB)
Header - Biol.Unit 1
Biol.Unit 2 (75 KB)
Header - Biol.Unit 2
Biol.Unit 3 (74 KB)
Header - Biol.Unit 3
Biol.Unit 4 (74 KB)
Header - Biol.Unit 4
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