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1MJJ
Biol. Unit 2
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Asym.Unit (160 KB)
Biol.Unit 1 (83 KB)
Biol.Unit 2 (77 KB)
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(1)
Title
:
HIGH RESOLUTION CRYSTAL STRUCTURE OF THE COMPLEX OF THE FAB FRAGMENT OF ESTEROLYTIC ANTIBODY MS6-12 AND A TRANSITION-STATE ANALOG
Authors
:
S. N. Ruzheinikov, T. A. Muranova, S. E. Sedelnikova, L. J. Partridge, G. M. Blackburn, I. A. Murray, H. Kakinuma, N. Takashi, K. Shimazaki, J. Sun, Y. Nishi, D. W. Rice
Date
:
28 Aug 02 (Deposition) - 23 Sep 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,H,L
Biol. Unit 1: A,B (1x)
Biol. Unit 2: H,L (1x)
Keywords
:
Catalytic Antibody, Ester Hydrolysis, Esterolytic, Fab, Immunoglobulin, Immune System
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. N. Ruzheinikov, T. A. Muranova, S. E. Sedelnikova, L. J. Partridge, G. M. Blackburn, I. A. Murray, H. Kakinuma, N. Takashi, K. Shimazaki, J. Sun, Y. Nishi, D. W. Rice
High-Resolution Crystal Structure Of The Fab-Fragments Of A Family Of Mouse Catalytic Antibodies With Esterase Activity
J. Mol. Biol. V. 332 423 2003
(for further references see the
PDB file header
)
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Hetero Components
(2, 2)
Info
All Hetero Components
1a: N-{[2-({[1-(4-CARBOXYBUTANOYL)AMIN... (HALa)
1b: N-{[2-({[1-(4-CARBOXYBUTANOYL)AMIN... (HALb)
2a: PYROGLUTAMIC ACID (PCAa)
2b: PYROGLUTAMIC ACID (PCAb)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
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No.
Name
Count
Type
Full Name
1
HAL
1
Ligand/Ion
N-{[2-({[1-(4-CARBOXYBUTANOYL)AMINO]-2-PHENYLETHYL}-HYDROXYPHOSPHINYL)OXY]ACETYL}-2-PHENYLETHYLAMINE
2
PCA
1
Mod. Amino Acid
PYROGLUTAMIC ACID
3
SO4
-1
Ligand/Ion
SULFATE ION
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Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC4 (SOFTWARE)
3: AC5 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG A:211 , ASN A:212 , HOH A:2224 , HOH A:2279 , SER L:203
BINDING SITE FOR RESIDUE SO4 A 2001
2
AC4
SOFTWARE
TYR A:32 , HIS A:91 , LEU A:92 , PHE A:96 , HOH A:2160 , HOH A:2203 , HOH A:2245 , TRP B:33 , ASN B:35 , ASN B:50 , LYS B:95 , HAL H:1002 , HOH L:347
BINDING SITE FOR RESIDUE HAL A 1001
3
AC5
SOFTWARE
HAL A:1001 , TRP H:33 , ASN H:35 , ASN H:50 , LYS H:95 , HOH H:1142 , TYR L:32 , HIS L:91 , LEU L:92 , TYR L:94 , PHE L:96 , HOH L:374 , HOH L:552
BINDING SITE FOR RESIDUE HAL H 1002
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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
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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_d1mjjb2 (B:114-228)
1b: SCOP_d1mjjh2 (H:114-227)
2a: SCOP_d1mjja2 (A:108-213)
2b: SCOP_d1mjjl2 (L:108-211)
3a: SCOP_d1mjjb1 (B:1-113)
3b: SCOP_d1mjjh1 (H:1-113)
4a: SCOP_d1mjja1 (A:1-107)
4b: SCOP_d1mjjl1 (L:1-107)
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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
d1mjjb2
B:114-228
1b
d1mjjh2
H:114-227
Protein domain
:
Immunoglobulin light chain kappa constant domain, CL-kappa
(495)
Mouse (Mus musculus) [TaxId: 10090]
(345)
2a
d1mjja2
A:108-213
2b
d1mjjl2
L:108-211
Family
:
V set domains (antibody variable domain-like)
(1919)
Protein domain
:
Immunoglobulin heavy chain variable domain, VH
(658)
Mouse (Mus musculus), cluster 3.2 [TaxId: 10090]
(177)
3a
d1mjjb1
B:1-113
3b
d1mjjh1
H:1-113
Protein domain
:
Immunoglobulin light chain kappa variable domain, VL-kappa
(616)
Mouse (Mus musculus), cluster 1.1 [TaxId: 10090]
(131)
4a
d1mjja1
A:1-107
4b
d1mjjl1
L:1-107
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CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_1mjjA02 (A:109-211)
1b: CATH_1mjjA01 (A:1-108)
1c: CATH_1mjjL01 (L:1-108)
1d: CATH_1mjjB02 (B:114-227)
1e: CATH_1mjjH02 (H:114-226)
1f: CATH_1mjjB01 (B:2-113)
1g: CATH_1mjjH01 (H:2-113)
1h: CATH_1mjjL02 (L:109-211)
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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
1mjjA02
A:109-211
1b
1mjjA01
A:1-108
1c
1mjjL01
L:1-108
1d
1mjjB02
B:114-227
1e
1mjjH02
H:114-226
1f
1mjjB01
B:2-113
1g
1mjjH01
H:2-113
1h
1mjjL02
L:109-211
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Pfam Domains
(0, 0)
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Asymmetric Unit 1
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Asym.Unit (160 KB)
Header - Asym.Unit
Biol.Unit 1 (83 KB)
Header - Biol.Unit 1
Biol.Unit 2 (77 KB)
Header - Biol.Unit 2
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