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1P7K
Biol. Unit 1
Info
Asym.Unit (163 KB)
Biol.Unit 1 (82 KB)
Biol.Unit 2 (79 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF AN ANTI-SSDNA ANTIGEN-BINDING FRAGMENT (FAB) BOUND TO 4-(2-HYDROXYETHYL)PIPERAZINE-1-ETHANESULFONIC ACID (HEPES)
Authors
:
J. P. Schuermann, M. T. Henzl, S. L. Deutscher, J. J. Tanner
Date
:
02 May 03 (Deposition) - 11 May 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.75
Chains
:
Asym. Unit : A,B,H,L
Biol. Unit 1: H,L (1x)
Biol. Unit 2: A,B (1x)
Keywords
:
Fab, Antibody, Anti-Dna Antibody, Autoantibody, Lupus, Hepes, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. P. Schuermann, M. T. Henzl, S. L. Deutscher, J. J. Tanner
Structure Of An Anti-Dna Fab Complexed With A Non-Dna Ligan Provides Insights Into Cross-Reactivity And Molecular Mimicry.
Proteins V. 57 269 2004
(for further references see the
PDB file header
)
[
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Hetero Components
(5, 19)
Info
All Hetero Components
1a: PENTAETHYLENE GLYCOL (1PEa)
1b: PENTAETHYLENE GLYCOL (1PEb)
1c: PENTAETHYLENE GLYCOL (1PEc)
1d: PENTAETHYLENE GLYCOL (1PEd)
2a: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEa)
2b: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEb)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
3e: GLYCEROL (GOLe)
3f: GLYCEROL (GOLf)
3g: GLYCEROL (GOLg)
3h: GLYCEROL (GOLh)
3i: GLYCEROL (GOLi)
3j: GLYCEROL (GOLj)
3k: GLYCEROL (GOLk)
3l: GLYCEROL (GOLl)
3m: GLYCEROL (GOLm)
3n: GLYCEROL (GOLn)
3o: GLYCEROL (GOLo)
3p: GLYCEROL (GOLp)
4a: DI(HYDROXYETHYL)ETHER (PEGa)
4b: DI(HYDROXYETHYL)ETHER (PEGb)
5a: SULFATE ION (SO4a)
5b: SULFATE ION (SO4b)
5c: SULFATE ION (SO4c)
5d: SULFATE ION (SO4d)
5e: SULFATE ION (SO4e)
5f: SULFATE ION (SO4f)
5g: SULFATE ION (SO4g)
5h: SULFATE ION (SO4h)
5i: SULFATE ION (SO4i)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
1PE
2
Ligand/Ion
PENTAETHYLENE GLYCOL
2
EPE
1
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3
GOL
8
Ligand/Ion
GLYCEROL
4
PEG
2
Ligand/Ion
DI(HYDROXYETHYL)ETHER
5
SO4
6
Ligand/Ion
SULFATE ION
[
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]
Sites
(23, 23)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC8 (SOFTWARE)
07: AC9 (SOFTWARE)
08: BC1 (SOFTWARE)
09: BC3 (SOFTWARE)
10: BC5 (SOFTWARE)
11: BC7 (SOFTWARE)
12: BC8 (SOFTWARE)
13: BC9 (SOFTWARE)
14: CC2 (SOFTWARE)
15: CC3 (SOFTWARE)
16: CC4 (SOFTWARE)
17: CC5 (SOFTWARE)
18: CC7 (SOFTWARE)
19: CC9 (SOFTWARE)
20: DC1 (SOFTWARE)
21: DC3 (SOFTWARE)
22: DC5 (SOFTWARE)
23: DC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
VAL H:2 , ARG H:94 , HOH H:1209
BINDING SITE FOR RESIDUE SO4 H 801
02
AC2
SOFTWARE
THR H:28 , SER H:31 , TYR H:32
BINDING SITE FOR RESIDUE SO4 H 802
03
AC3
SOFTWARE
LYS H:58 , TYR H:100A , HOH H:1342 , GLY L:93 , THR L:94 , EPE L:901
BINDING SITE FOR RESIDUE SO4 H 803
04
AC4
SOFTWARE
SER H:25 , GLY H:26 , TYR H:97 , HOH H:1311
BINDING SITE FOR RESIDUE SO4 H 804
05
AC5
SOFTWARE
LYS A:52 , HOH A:1263 , SER H:158 , LEU H:159 , SER H:160 , SER H:161 , HOH H:1347
BINDING SITE FOR RESIDUE SO4 H 805
06
AC8
SOFTWARE
LYS H:73 , ARG L:108
BINDING SITE FOR RESIDUE SO4 L 808
07
AC9
SOFTWARE
TYR B:27 , THR B:28 , TYR B:32 , HOH L:1364
BINDING SITE FOR RESIDUE SO4 B 809
08
BC1
SOFTWARE
ARG H:98 , PRO H:99 , TYR H:100 , TYR H:100A , SO4 H:803 , TYR L:32 , HIS L:91 , TYR L:92 , HOH L:1294
BINDING SITE FOR RESIDUE EPE L 901
09
BC3
SOFTWARE
TYR H:50 , ASN H:52 , TYR H:53 , ASN H:54 , TYR H:100 , PEG H:1202 , HOH H:1331 , HOH H:1339
BINDING SITE FOR RESIDUE 1PE H 1001
10
BC5
SOFTWARE
TYR B:53 , SER L:31 , LYS L:52 , SER L:65 , GLY L:66 , SER L:67 , GLN L:70 , SER L:72
BINDING SITE FOR RESIDUE 1PE L 1003
11
BC7
SOFTWARE
PRO B:14 , SER B:84 , ASP B:173 , HOH B:1221 , ILE L:150 , ASP L:151 , SER L:153 , ARG L:155 , HOH L:1223
BINDING SITE FOR RESIDUE PEG L 1201
12
BC8
SOFTWARE
SER H:31 , TYR H:97 , 1PE H:1001
BINDING SITE FOR RESIDUE PEG H 1202
13
BC9
SOFTWARE
LYS H:38 , GLU H:46 , LYS H:62 , PHE H:63 , HOH H:1279 , HOH H:1365
BINDING SITE FOR RESIDUE GOL H 1101
14
CC2
SOFTWARE
VAL A:15 , GLY A:16 , HOH A:1198 , SER L:31 , TYR L:32 , ASN L:50 , HOH L:1319 , HOH L:1337 , HOH L:1338
BINDING SITE FOR RESIDUE GOL L 1103
15
CC3
SOFTWARE
LYS H:38 , GLN H:39 , LYS H:40 , GLN H:43 , GLY H:44 , GLU H:46 , HOH H:1328
BINDING SITE FOR RESIDUE GOL H 1105
16
CC4
SOFTWARE
PHE H:166 , PRO H:167 , THR H:176 , LEU H:177 , SER H:178 , HOH H:1215 , SER L:162 , SER L:176 , THR L:178
BINDING SITE FOR RESIDUE GOL H 1106
17
CC5
SOFTWARE
PRO L:8 , ALA L:9 , SER L:10 , HOH L:1277
BINDING SITE FOR RESIDUE GOL L 1107
18
CC7
SOFTWARE
GLY H:127 , SER H:128 , ARG H:213 , PRO L:119 , PHE L:209 , ASN L:210 , ARG L:211 , HOH L:1311
BINDING SITE FOR RESIDUE GOL L 1110
19
CC9
SOFTWARE
ARG A:108 , LYS B:73 , HOH L:1421
BINDING SITE FOR RESIDUE GOL B 1112
20
DC1
SOFTWARE
TYR H:91 , GLN L:38 , LYS L:39 , GLY L:41 , LYS L:42 , HOH L:1247 , HOH L:1386
BINDING SITE FOR RESIDUE GOL L 1115
21
DC3
SOFTWARE
SER A:127 , HOH A:1169 , SER B:120 , TYR B:122 , SER H:120 , HOH H:1260 , HOH H:1291
BINDING SITE FOR RESIDUE GOL B 1117
22
DC5
SOFTWARE
GLN L:37 , GLY L:57 , PRO L:59 , HOH L:1205 , HOH L:1414
BINDING SITE FOR RESIDUE GOL L 1119
23
DC6
SOFTWARE
PHE A:83 , GLN A:166 , HOH A:1163 , TYR L:30
BINDING SITE FOR RESIDUE GOL A 1120
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: IG_MHC (L:192-198)
;
View:
Select:
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_MOUSE
84-90
1
-
L:192-198
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
View:
Label:
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_d1p7kb2 (B:114-214)
1b: SCOP_d1p7kh2 (H:114-215)
2a: SCOP_d1p7ka2 (A:108-214)
2b: SCOP_d1p7kl2 (L:108-213)
3a: SCOP_d1p7kb1 (B:1-113)
3b: SCOP_d1p7kh1 (H:1-113)
4a: SCOP_d1p7ka1 (A:1-107)
4b: SCOP_d1p7kl1 (L:1-107)
View:
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Classes
(
)
(
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Folds
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)
(
)
Superfamilies
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)
(
)
Families
(
)
(
)
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
d1p7kb2
B:114-214
1b
d1p7kh2
H:114-215
Protein domain
:
Immunoglobulin light chain kappa constant domain, CL-kappa
(495)
Mouse (Mus musculus) [TaxId: 10090]
(345)
2a
d1p7ka2
A:108-214
2b
d1p7kl2
L:108-213
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
d1p7kb1
B:1-113
3b
d1p7kh1
H:1-113
Protein domain
:
Immunoglobulin light chain kappa variable domain, VL-kappa
(616)
Mouse (Mus musculus), cluster 4 [TaxId: 10090]
(211)
4a
d1p7ka1
A:1-107
4b
d1p7kl1
L:1-107
[
close SCOP info
]
CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_1p7kL02 (L:109-212)
1b: CATH_1p7kH02 (H:114-211)
1c: CATH_1p7kB02 (B:114-211)
1d: CATH_1p7kA02 (A:109-211)
1e: CATH_1p7kH01 (H:2-113)
1f: CATH_1p7kB01 (B:1-113)
1g: CATH_1p7kA01 (A:1-108)
1h: CATH_1p7kL01 (L:1-108)
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Classes
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(
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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)
House mouse (Mus musculus)
(616)
1a
1p7kL02
L:109-212
1b
1p7kH02
H:114-211
1c
1p7kB02
B:114-211
1d
1p7kA02
A:109-211
1e
1p7kH01
H:2-113
1f
1p7kB01
B:1-113
1g
1p7kA01
A:1-108
1h
1p7kL01
L:1-108
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Asym.Unit (163 KB)
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