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2W08
Asym. Unit
Info
Asym.Unit (207 KB)
Biol.Unit 1 (200 KB)
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(1)
Title
:
THE STRUCTURE OF SERUM AMYLOID P COMPONENT BOUND TO 0-PHOSPHO-THREONINE
Authors
:
S. E. Kolstoe, M. B. Pepys, S. P. Wood
Date
:
12 Aug 08 (Deposition) - 14 Apr 09 (Release) - 19 May 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.70
Chains
:
Asym. Unit : A,B,C,D,E
Biol. Unit 1: A,B,C,D,E (1x)
Keywords
:
Glycoprotein, Polymorphism, Metal-Binding, Tau, Lectin, Calcium, Amyloid, Secreted, Alzheimers
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. E. Kolstoe, B. H. Ridha, V. Bellotti, N. Wang, C. V. Robinson, S. J. Crutch, G. Keir, R. Kukkastenvehmas, J. R. Gallimore, W. L. Hutchinson, P. N. Hawkins, S. P. Wood, M. N. Rossor, M. B. Pepys
Molecular Dissection Of Alzheimer'S Disease Neuropathology By Depletion Of Serum Amyloid P Component.
Proc. Natl. Acad. Sci. Usa V. 106 7619 2009
[
close entry info
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Hetero Components
(3, 20)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
1e: CALCIUM ION (CAe)
1f: CALCIUM ION (CAf)
1g: CALCIUM ION (CAg)
1h: CALCIUM ION (CAh)
1i: CALCIUM ION (CAi)
1j: CALCIUM ION (CAj)
2a: N-ACETYL-D-GLUCOSAMINE (NAGa)
2b: N-ACETYL-D-GLUCOSAMINE (NAGb)
2c: N-ACETYL-D-GLUCOSAMINE (NAGc)
2d: N-ACETYL-D-GLUCOSAMINE (NAGd)
2e: N-ACETYL-D-GLUCOSAMINE (NAGe)
3a: PHOSPHOTHREONINE (TPOa)
3b: PHOSPHOTHREONINE (TPOb)
3c: PHOSPHOTHREONINE (TPOc)
3d: PHOSPHOTHREONINE (TPOd)
3e: PHOSPHOTHREONINE (TPOe)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
10
Ligand/Ion
CALCIUM ION
2
NAG
5
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
3
TPO
5
Mod. Residue
PHOSPHOTHREONINE
[
close Hetero Component info
]
Sites
(20, 20)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:58 , ASN A:59 , GLU A:136 , GLN A:137 , ASP A:138 , TPO A:500
BINDING SITE FOR RESIDUE CA A 205
02
AC2
SOFTWARE
GLU A:136 , ASP A:138 , GLN A:148 , TPO A:500 , HOH A:2184 , HOH A:2192
BINDING SITE FOR RESIDUE CA A 206
03
AC3
SOFTWARE
GLN A:31 , ASN A:32 , GLU A:99 , SER A:101 , HOH A:2058 , HOH A:2150 , HOH A:2258
BINDING SITE FOR RESIDUE NAG A 207
04
AC4
SOFTWARE
ASP A:58 , ASN A:59 , LEU A:62 , TYR A:64 , TYR A:74 , GLU A:136 , ASP A:138 , GLN A:148 , CA A:205 , CA A:206 , HOH A:2101 , HOH A:2106 , HOH A:2259 , HOH A:2260 , HOH A:2261
BINDING SITE FOR RESIDUE TPO A 500
05
AC5
SOFTWARE
GLU B:136 , ASP B:138 , GLN B:148 , TPO B:500 , HOH B:2186 , HOH B:2200
BINDING SITE FOR RESIDUE CA B 205
06
AC6
SOFTWARE
ASP B:58 , ASN B:59 , GLU B:136 , GLN B:137 , ASP B:138 , TPO B:500
BINDING SITE FOR RESIDUE CA B 206
07
AC7
SOFTWARE
GLN B:31 , ASN B:32 , GLU B:99 , HOH B:2059
BINDING SITE FOR RESIDUE NAG B 207
08
AC8
SOFTWARE
ASP B:58 , ASN B:59 , LEU B:62 , TYR B:74 , GLU B:136 , ASP B:138 , GLN B:148 , CA B:205 , CA B:206 , HOH B:2101 , HOH B:2267 , HOH B:2268 , HOH B:2269 , HOH B:2270
BINDING SITE FOR RESIDUE TPO B 500
09
AC9
SOFTWARE
ASP C:58 , ASN C:59 , GLU C:136 , GLN C:137 , ASP C:138 , TPO C:500
BINDING SITE FOR RESIDUE CA C 205
10
BC1
SOFTWARE
GLU C:136 , ASP C:138 , GLN C:148 , TPO C:500 , HOH C:2190 , HOH C:2199
BINDING SITE FOR RESIDUE CA C 206
11
BC2
SOFTWARE
GLN C:31 , ASN C:32 , GLU C:99 , HOH C:2214 , HOH C:2269
BINDING SITE FOR RESIDUE NAG C 207
12
BC3
SOFTWARE
ASP C:58 , ASN C:59 , LEU C:62 , TYR C:74 , GLU C:136 , ASP C:138 , GLN C:148 , CA C:205 , CA C:206 , HOH C:2101 , HOH C:2117 , HOH C:2271 , HOH C:2272 , HOH C:2273
BINDING SITE FOR RESIDUE TPO C 500
13
BC4
SOFTWARE
GLU D:136 , ASP D:138 , GLN D:148 , TPO D:500 , HOH D:2176 , HOH D:2190
BINDING SITE FOR RESIDUE CA D 205
14
BC5
SOFTWARE
ASP D:58 , ASN D:59 , GLU D:136 , GLN D:137 , ASP D:138 , TPO D:500
BINDING SITE FOR RESIDUE CA D 206
15
BC6
SOFTWARE
GLN D:31 , ASN D:32 , GLU D:99 , HOH D:2055 , HOH D:2140 , HOH D:2265
BINDING SITE FOR RESIDUE NAG D 207
16
BC7
SOFTWARE
ASP D:58 , ASN D:59 , LEU D:62 , TYR D:74 , GLU D:136 , ASP D:138 , GLN D:148 , CA D:205 , CA D:206 , HOH D:2266 , HOH D:2267
BINDING SITE FOR RESIDUE TPO D 500
17
BC8
SOFTWARE
ASP E:58 , ASN E:59 , GLU E:136 , GLN E:137 , ASP E:138 , TPO E:500
BINDING SITE FOR RESIDUE CA E 205
18
BC9
SOFTWARE
GLU E:136 , ASP E:138 , GLN E:148 , TPO E:500 , HOH E:2188 , HOH E:2201
BINDING SITE FOR RESIDUE CA E 206
19
CC1
SOFTWARE
GLN E:31 , ASN E:32 , GLU E:99 , HOH E:2056 , HOH E:2277 , HOH E:2278 , HOH E:2279
BINDING SITE FOR RESIDUE NAG E 207
20
CC2
SOFTWARE
ASP E:58 , ASN E:59 , LEU E:62 , TYR E:74 , GLU E:136 , ASP E:138 , GLN E:148 , CA E:205 , CA E:206 , HOH E:2097 , HOH E:2109 , HOH E:2128 , HOH E:2280 , HOH E:2281 , HOH E:2282
BINDING SITE FOR RESIDUE TPO E 500
[
close Site info
]
SAPs(SNPs)/Variants
(3, 15)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_035814 (G122S, chain A/B/C/D/E, )
2: VAR_006054 (E136G, chain A/B/C/D/E, )
3: VAR_006055 (S139G, chain A/B/C/D/E, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_035814
G
141
S
SAMP_HUMAN
Unclassified
---
A/B/C/D/E
G
122
S
2
UniProt
VAR_006054
E
155
G
SAMP_HUMAN
Polymorphism
---
A/B/C/D/E
E
136
G
3
UniProt
VAR_006055
S
158
G
SAMP_HUMAN
Polymorphism
---
A/B/C/D/E
S
139
G
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 10)
Info
All PROSITE Patterns/Profiles
1: PTX_2 (A:5-204,B:5-204,C:5-204,D:5-204,E:...)
2: PTX_1 (A:93-100,B:93-100,C:93-100,D:93-10...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PTX_2
PS51828
Pentraxin (PTX) domain profile.
SAMP_HUMAN
24-223
5
A:5-204
B:5-204
C:5-204
D:5-204
E:5-204
2
PTX_1
PS00289
Pentraxin domain signature.
SAMP_HUMAN
112-119
5
A:93-100
B:93-100
C:93-100
D:93-100
E:93-100
[
close PROSITE info
]
Exons
(2, 10)
Info
All Exons
Exon 1.1 (A:1-3 | B:1-3 | C:1-3 | D:1-3 | E:...)
Exon 1.2 (A:3-204 | B:3-204 | C:3-204 | D:3-...)
View:
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All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/1.2
3: Boundary 1.2/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1
ENST00000255040
1
ENSE00000904938
chr1:
159557615-159557775
161
SAMP_HUMAN
1-22
22
5
A:1-3
B:1-3
C:1-3
D:1-3
E:1-3
3
3
3
3
3
1.2
ENST00000255040
2
ENSE00000904939
chr1:
159557891-159558655
765
SAMP_HUMAN
22-223
202
5
A:3-204
B:3-204
C:3-204
D:3-204
E:3-204
202
202
202
202
202
[
close EXON info
]
SCOP Domains
(1, 5)
Info
All SCOP Domains
1a: SCOP_d2w08a_ (A:)
1b: SCOP_d2w08b_ (B:)
1c: SCOP_d2w08c_ (C:)
1d: SCOP_d2w08d_ (D:)
1e: SCOP_d2w08e_ (E:)
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)
(
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(
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(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Concanavalin A-like lectins/glucanases
(797)
Superfamily
:
Concanavalin A-like lectins/glucanases
(797)
Family
:
Pentraxin (pentaxin)
(18)
Protein domain
:
Serum amyloid P component (SAP)
(12)
Human (Homo sapiens) [TaxId: 9606]
(12)
1a
d2w08a_
A:
1b
d2w08b_
B:
1c
d2w08c_
C:
1d
d2w08d_
D:
1e
d2w08e_
E:
[
close SCOP info
]
CATH Domains
(1, 5)
Info
all CATH domains
1a: CATH_2w08A00 (A:1-204)
1b: CATH_2w08B00 (B:1-204)
1c: CATH_2w08C00 (C:1-204)
1d: CATH_2w08D00 (D:1-204)
1e: CATH_2w08E00 (E:1-204)
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)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Jelly Rolls
(1293)
Homologous Superfamily
:
[code=2.60.120.200, no name defined]
(421)
Human (Homo sapiens)
(49)
1a
2w08A00
A:1-204
1b
2w08B00
B:1-204
1c
2w08C00
C:1-204
1d
2w08D00
D:1-204
1e
2w08E00
E:1-204
[
close CATH info
]
Pfam Domains
(1, 5)
Info
all PFAM domains
1a: PFAM_Pentaxin_2w08E01 (E:7-200)
1b: PFAM_Pentaxin_2w08E02 (E:7-200)
1c: PFAM_Pentaxin_2w08E03 (E:7-200)
1d: PFAM_Pentaxin_2w08E04 (E:7-200)
1e: PFAM_Pentaxin_2w08E05 (E:7-200)
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Clans
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Families
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)
Organisms
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)
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)
Clan
:
Concanavalin
(293)
Family
:
Pentaxin
(6)
Homo sapiens (Human)
(6)
1a
Pentaxin-2w08E01
E:7-200
1b
Pentaxin-2w08E02
E:7-200
1c
Pentaxin-2w08E03
E:7-200
1d
Pentaxin-2w08E04
E:7-200
1e
Pentaxin-2w08E05
E:7-200
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