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1WCB
Biol. Unit 2
Info
Asym.Unit (153 KB)
Biol.Unit 1 (76 KB)
Biol.Unit 2 (75 KB)
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(1)
Title
:
PLP-DEPENDENT CATALYTIC ANTIBODY 15A9 IN COMPLEX WITH ITS HAPTEN
Authors
:
B. Golinelli-Pimpaneau, P. Christen
Date
:
12 Nov 04 (Deposition) - 03 Mar 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,H,L
Biol. Unit 1: A,B (1x)
Biol. Unit 2: H,L (1x)
Keywords
:
Catalytic Antibody, Transamination, Pyridoxal-Phosphate, Hapten, Phosphopyridoxyl-L-Lysine, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. Golinelli-Pimpaneau, C. Luthi, P. Christen
Structural Basis For D-Amino Acid Transamination By The Pyridoxal- 5' -Phosphate - Dependent Catalytic Antibody 15A9.
J. Biol. Chem. V. 281 23969 2006
(for further references see the
PDB file header
)
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Hetero Components
(2, 6)
Info
All Hetero Components
1a: IODIDE ION (IODa)
1b: IODIDE ION (IODb)
1c: IODIDE ION (IODc)
1d: IODIDE ION (IODd)
1e: IODIDE ION (IODe)
1f: IODIDE ION (IODf)
1g: IODIDE ION (IODg)
1h: IODIDE ION (IODh)
1i: IODIDE ION (IODi)
2a: N~2~-({3-HYDROXY-2-METHYL-5-[(PHOS... (PE1a)
2b: N~2~-({3-HYDROXY-2-METHYL-5-[(PHOS... (PE1b)
View:
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Label:
No.
Name
Count
Type
Full Name
1
IOD
5
Ligand/Ion
IODIDE ION
2
PE1
1
Ligand/Ion
N~2~-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-L-LYSINE
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Sites
(7, 7)
Info
All Sites
1: AC4 (SOFTWARE)
2: AC5 (SOFTWARE)
3: AC6 (SOFTWARE)
4: AC7 (SOFTWARE)
5: AC8 (SOFTWARE)
6: AC9 (SOFTWARE)
7: BC1 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC4
SOFTWARE
GLY H:97 , TYR H:99 , ASN H:100A , TRP H:100E
BINDING SITE FOR RESIDUE IOD H1213
2
AC5
SOFTWARE
VAL A:206 , SER A:208 , ALA H:84
BINDING SITE FOR RESIDUE IOD H1214
3
AC6
SOFTWARE
ARG H:71
BINDING SITE FOR RESIDUE IOD H1215
4
AC7
SOFTWARE
LYS H:96
BINDING SITE FOR RESIDUE IOD H1216
5
AC8
SOFTWARE
GLU B:85 , SER L:191
BINDING SITE FOR RESIDUE IOD L1215
6
AC9
SOFTWARE
TYR A:32 , HIS A:34 , SER A:50 , ARG A:91 , SER A:92 , TYR A:94 , PHE A:96 , HOH A:2065 , HOH A:2121 , TYR B:33 , ARG B:52 , ASP B:95 , LYS B:96 , TYR B:100B , TRP B:100E , SER H:161 , HOH H:2100 , LYS L:169
BINDING SITE FOR RESIDUE PE1 A1215
7
BC1
SOFTWARE
LYS A:169 , SER B:161 , HOH B:2103 , TYR H:33 , ARG H:52 , ASP H:95 , TYR H:100B , TRP H:100E , TYR L:32 , HIS L:34 , SER L:50 , ARG L:91 , TYR L:94 , HOH L:2049 , HOH L:2105 , HOH L:2106 , HOH L:2107
BINDING SITE FOR RESIDUE PE1 L1216
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
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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_d1wcba1 (A:1-107)
1b: SCOP_d1wcbl1 (L:1-107)
2a: SCOP_d1wcba2 (A:108-214)
2b: SCOP_d1wcbl2 (L:108-214)
3a: SCOP_d1wcbb2 (B:114-214)
3b: SCOP_d1wcbh2 (H:114-213)
4a: SCOP_d1wcbb1 (B:1-113)
4b: SCOP_d1wcbh1 (H:1-113)
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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)
Mouse (Mus musculus) [TaxId: 10090]
(360)
1a
d1wcba1
A:1-107
1b
d1wcbl1
L:1-107
Family
:
C1 set domains (antibody constant domain-like)
(3013)
Protein domain
:
automated matches
(652)
Mouse (Mus musculus) [TaxId: 10090]
(309)
2a
d1wcba2
A:108-214
2b
d1wcbl2
L:108-214
Protein domain
:
Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma
(608)
Mouse (Mus musculus) [TaxId: 10090]
(414)
3a
d1wcbb2
B:114-214
3b
d1wcbh2
H:114-213
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)
4a
d1wcbb1
B:1-113
4b
d1wcbh1
H:1-113
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CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_1wcbA02 (A:109-214)
1b: CATH_1wcbL02 (L:109-214)
1c: CATH_1wcbA01 (A:1-108)
1d: CATH_1wcbL01 (L:1-108)
1e: CATH_1wcbB02 (B:114-214)
1f: CATH_1wcbH02 (H:114-213)
1g: CATH_1wcbB01 (B:1-113)
1h: CATH_1wcbH01 (H:1-113)
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Organisms
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(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Mouse (Mus musculus)
(152)
1a
1wcbA02
A:109-214
1b
1wcbL02
L:109-214
1c
1wcbA01
A:1-108
1d
1wcbL01
L:1-108
1e
1wcbB02
B:114-214
1f
1wcbH02
H:114-213
1g
1wcbB01
B:1-113
1h
1wcbH01
H:1-113
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Pfam Domains
(0, 0)
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Asymmetric Unit 1
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Show PDB file:
Asym.Unit (153 KB)
Header - Asym.Unit
Biol.Unit 1 (76 KB)
Header - Biol.Unit 1
Biol.Unit 2 (75 KB)
Header - Biol.Unit 2
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