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1RU9
Asym. Unit
Info
Asym.Unit (81 KB)
Biol.Unit 1 (76 KB)
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(1)
Title
:
CRYSTAL STRUCTURE (A) OF U.V.-IRRADIATED CATIONIC CYCLIZATION ANTIBODY 4C6 FAB AT PH 4.6 WITH A DATA SET COLLECTED IN-HOUSE.
Authors
:
X. Zhu, P. Wentworth Jr. , A. D. Wentworth, A. Eschenmoser, R. A. Lerner I. A. Wilson
Date
:
11 Dec 03 (Deposition) - 02 Mar 04 (Release) - 05 Jun 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : H,L
Biol. Unit 1: H,L (1x)
Keywords
:
Immunoglobulin, Catalytic Antibody, Water Oxidation, Amino Acid Modification, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
X. Zhu, P. Wentworth Jr. , A. D. Wentworth, A. Eschenmoser, R. A. Lerner, I. A. Wilson
Probing The Antibody-Catalyzed Water-Oxidation Pathway At Atomic Resolution.
Proc. Natl. Acad. Sci. Usa V. 110 2247 2004
(for further references see the
PDB file header
)
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Hetero Components
(5, 9)
Info
All Hetero Components
1a: 4-HYDROXYTRYPTOPHAN (4HTa)
2a: ACETATE ION (ACTa)
3a: BENZOIC ACID (BEZa)
4a: (2S,4S)-2,5-DIAMINO-4-HYDROXY-5-OX... (GHGa)
5a: GLYCEROL (GOLa)
5b: GLYCEROL (GOLb)
5c: GLYCEROL (GOLc)
5d: GLYCEROL (GOLd)
5e: GLYCEROL (GOLe)
View:
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Label:
No.
Name
Count
Type
Full Name
1
4HT
1
Mod. Amino Acid
4-HYDROXYTRYPTOPHAN
2
ACT
1
Ligand/Ion
ACETATE ION
3
BEZ
1
Ligand/Ion
BENZOIC ACID
4
GHG
1
Mod. Amino Acid
(2S,4S)-2,5-DIAMINO-4-HYDROXY-5-OXOPENTANOIC ACID (NON-PREFERRED NAME)
5
GOL
5
Ligand/Ion
GLYCEROL
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Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
LEU H:95 , TRP H:103 , HOH H:712 , ASN L:34 , LEU L:36
BINDING SITE FOR RESIDUE ACT H 611
2
AC2
SOFTWARE
ALA H:34 , ASN H:35A , TYR H:50 , LEU H:95 , LEU H:96 , PRO H:230 , PHE L:32 , TRP L:89 , GLY L:91
BINDING SITE FOR RESIDUE BEZ H 601
3
AC3
SOFTWARE
LYS H:44 , LEU H:45 , THR L:97 , PHE L:98 , HOH L:624
BINDING SITE FOR RESIDUE GOL H 621
4
AC4
SOFTWARE
PHE H:174 , PRO H:175 , THR H:186 , SER H:188 , SER L:176 , THR L:178
BINDING SITE FOR RESIDUE GOL L 622
5
AC5
SOFTWARE
ARG H:71 , ASP H:72 , THR H:73 , LEU L:54
BINDING SITE FOR RESIDUE GOL H 623
6
AC6
SOFTWARE
VAL H:12 , GLN H:16 , SER H:17 , ASP H:32 , TYR H:53 , TRP H:97 , HOH H:627 , HOH H:644
BINDING SITE FOR RESIDUE GOL H 624
7
AC7
SOFTWARE
VAL H:121 , TYR H:122 , SER H:215 , LYS H:221 , HOH H:666 , HOH H:727 , GLU L:123
BINDING SITE FOR RESIDUE GOL H 625
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are not available)
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PROSITE Patterns/Profiles
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Exons
(0, 0)
Info
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(4, 4)
Info
All SCOP Domains
1a: SCOP_d1ru9h2 (H:114-231)
2a: SCOP_d1ru9l2 (L:108-214)
3a: SCOP_d1ru9h1 (H:1-113)
4a: SCOP_d1ru9l1 (L:1-107)
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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
d1ru9h2
H:114-231
Protein domain
:
Immunoglobulin light chain kappa constant domain, CL-kappa
(495)
Mouse (Mus musculus) [TaxId: 10090]
(345)
2a
d1ru9l2
L:108-214
Family
:
V set domains (antibody variable domain-like)
(1919)
Protein domain
:
Immunoglobulin heavy chain variable domain, VH
(658)
Mouse (Mus musculus), cluster 7.1 [TaxId: 10090]
(38)
3a
d1ru9h1
H:1-113
Protein domain
:
Immunoglobulin light chain kappa variable domain, VL-kappa
(616)
Mouse (Mus musculus), cluster 1.1 [TaxId: 10090]
(131)
4a
d1ru9l1
L:1-107
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1ru9L02 (L:109-214)
1b: CATH_1ru9L01 (L:1-108)
1c: CATH_1ru9H02 (H:114-227)
1d: CATH_1ru9H01 (H:1-113)
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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
1ru9L02
L:109-214
1b
1ru9L01
L:1-108
1c
1ru9H02
H:114-227
1d
1ru9H01
H:1-113
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Pfam Domains
(0, 0)
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Asymmetric Unit 1
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Asym.Unit (81 KB)
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