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1SAC
Asym. Unit
Info
Asym.Unit (174 KB)
Biol.Unit 1 (167 KB)
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(1)
Title
:
THE STRUCTURE OF PENTAMERIC HUMAN SERUM AMYLOID P COMPONENT
Authors
:
H. E. White, J. Emsley, B. P. O'Hara, G. Oliva, N. Srinivasan, I. J. Tickle, T. L. Blundell, M. B. Pepys, S. P. Wood
Date
:
27 Jan 94 (Deposition) - 31 May 94 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D,E
Biol. Unit 1: A,B,C,D,E (1x)
Keywords
:
Amyloid Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Emsley, H. E. White, B. P. O'Hara, G. Oliva, N. Srinivasan, I. J. Tickle, T. L. Blundell, M. B. Pepys, S. P. Wood
Structure Of Pentameric Human Serum Amyloid P Component.
Nature V. 367 338 1994
(for further references see the
PDB file header
)
[
close entry info
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Hetero Components
(2, 14)
Info
All Hetero Components
1a: ACETIC ACID (ACYa)
1b: ACETIC ACID (ACYb)
1c: ACETIC ACID (ACYc)
1d: ACETIC ACID (ACYd)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
2d: CALCIUM ION (CAd)
2e: CALCIUM ION (CAe)
2f: CALCIUM ION (CAf)
2g: CALCIUM ION (CAg)
2h: CALCIUM ION (CAh)
2i: CALCIUM ION (CAi)
2j: CALCIUM ION (CAj)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACY
4
Ligand/Ion
ACETIC ACID
2
CA
10
Ligand/Ion
CALCIUM ION
[
close Hetero Component info
]
Sites
(24, 24)
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: C1A (UNKNOWN)
16: C1B (UNKNOWN)
17: C1C (UNKNOWN)
18: C1D (UNKNOWN)
19: C1E (UNKNOWN)
20: C2A (UNKNOWN)
21: C2B (UNKNOWN)
22: C2C (UNKNOWN)
23: C2D (UNKNOWN)
24: C2E (UNKNOWN)
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 , ACY A:300
BINDING SITE FOR RESIDUE CA A 205
02
AC2
SOFTWARE
GLU A:136 , ASP A:138 , GLN A:148 , ACY A:300
BINDING SITE FOR RESIDUE CA A 206
03
AC3
SOFTWARE
ASP B:58 , ASN B:59 , GLU B:136 , GLN B:137 , ASP B:138 , ACY B:300
BINDING SITE FOR RESIDUE CA B 205
04
AC4
SOFTWARE
GLU B:136 , ASP B:138 , GLN B:148 , ACY B:300
BINDING SITE FOR RESIDUE CA B 206
05
AC5
SOFTWARE
GLU A:167 , ASP C:58 , ASN C:59 , GLU C:136 , GLN C:137 , ASP C:138
BINDING SITE FOR RESIDUE CA C 205
06
AC6
SOFTWARE
GLU A:167 , GLU C:136 , ASP C:138 , GLN C:148
BINDING SITE FOR RESIDUE CA C 206
07
AC7
SOFTWARE
ASP D:58 , ASN D:59 , GLU D:136 , GLN D:137 , ASP D:138 , ACY D:300
BINDING SITE FOR RESIDUE CA D 205
08
AC8
SOFTWARE
GLU D:136 , ASP D:138 , GLN D:148 , ACY D:300
BINDING SITE FOR RESIDUE CA D 206
09
AC9
SOFTWARE
ASP E:58 , ASN E:59 , GLU E:136 , GLN E:137 , ASP E:138 , ACY E:300
BINDING SITE FOR RESIDUE CA E 205
10
BC1
SOFTWARE
GLU E:136 , ASP E:138 , GLN E:148 , ACY E:300
BINDING SITE FOR RESIDUE CA E 206
11
BC2
SOFTWARE
ASP A:58 , ASN A:59 , GLU A:136 , ASP A:138 , GLN A:148 , CA A:205 , CA A:206
BINDING SITE FOR RESIDUE ACY A 300
12
BC3
SOFTWARE
ASP B:58 , ASN B:59 , GLU B:136 , ASP B:138 , GLN B:148 , CA B:205 , CA B:206
BINDING SITE FOR RESIDUE ACY B 300
13
BC4
SOFTWARE
ASP D:58 , ASN D:59 , GLU D:136 , ASP D:138 , GLN D:148 , CA D:205 , CA D:206
BINDING SITE FOR RESIDUE ACY D 300
14
BC5
SOFTWARE
ASP E:58 , ASN E:59 , GLU E:136 , ASP E:138 , GLN E:148 , CA E:205 , CA E:206
BINDING SITE FOR RESIDUE ACY E 300
15
C1A
UNKNOWN
ASP A:58 , ASN A:59 , GLU A:136 , GLN A:137 , ASP A:138 , ACY A:300
NULL
16
C1B
UNKNOWN
ASP B:58 , ASN B:59 , GLU B:136 , GLN B:137 , ASP B:138 , ACY B:300
NULL
17
C1C
UNKNOWN
ASP C:58 , ASN C:59 , GLU C:136 , GLN C:137 , ASP C:138
NULL
18
C1D
UNKNOWN
ASP D:58 , ASN D:59 , GLU D:136 , GLN D:137 , ASP D:138 , ACY D:300
NULL
19
C1E
UNKNOWN
ASP E:58 , ASN E:59 , GLU E:136 , GLN E:137 , ASP E:138 , ACY E:300
NULL
20
C2A
UNKNOWN
GLU A:136 , ASP A:138 , GLN A:148 , ACY A:300
NULL
21
C2B
UNKNOWN
GLU B:136 , ASP B:138 , GLN B:148 , ACY B:300
NULL
22
C2C
UNKNOWN
GLU C:136 , ASP C:138 , GLN C:148
NULL
23
C2D
UNKNOWN
GLU D:136 , ASP D:138 , GLN D:148 , ACY D:300
NULL
24
C2E
UNKNOWN
GLU E:136 , ASP E:138 , GLN E:148 , ACY E:300
NULL
[
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)
[
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]
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
[
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]
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_d1saca_ (A:)
1b: SCOP_d1sacb_ (B:)
1c: SCOP_d1sacc_ (C:)
1d: SCOP_d1sacd_ (D:)
1e: SCOP_d1sace_ (E:)
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)
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
d1saca_
A:
1b
d1sacb_
B:
1c
d1sacc_
C:
1d
d1sacd_
D:
1e
d1sace_
E:
[
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]
CATH Domains
(1, 5)
Info
all CATH domains
1a: CATH_1sacA00 (A:1-204)
1b: CATH_1sacC00 (C:1-204)
1c: CATH_1sacD00 (D:1-204)
1d: CATH_1sacE00 (E:1-204)
1e: CATH_1sacB00 (B: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
1sacA00
A:1-204
1b
1sacC00
C:1-204
1c
1sacD00
D:1-204
1d
1sacE00
E:1-204
1e
1sacB00
B:1-204
[
close CATH info
]
Pfam Domains
(1, 5)
Info
all PFAM domains
1a: PFAM_Pentaxin_1sacE01 (E:7-200)
1b: PFAM_Pentaxin_1sacE02 (E:7-200)
1c: PFAM_Pentaxin_1sacE03 (E:7-200)
1d: PFAM_Pentaxin_1sacE04 (E:7-200)
1e: PFAM_Pentaxin_1sacE05 (E:7-200)
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Clans
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)
Organisms
(
)
(
)
Clan
:
Concanavalin
(293)
Family
:
Pentaxin
(6)
Homo sapiens (Human)
(6)
1a
Pentaxin-1sacE01
E:7-200
1b
Pentaxin-1sacE02
E:7-200
1c
Pentaxin-1sacE03
E:7-200
1d
Pentaxin-1sacE04
E:7-200
1e
Pentaxin-1sacE05
E:7-200
[
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]
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Asym.Unit (174 KB)
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