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2A3Y
Asym. Unit
Info
Asym.Unit (184 KB)
Biol.Unit 1 (177 KB)
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(1)
Title
:
PENTAMERIC CRYSTAL STRUCTURE OF HUMAN SERUM AMYLOID P-COMPONENT BOUND TO BIS-1,2-{[(Z)-2CARBOXY-2-METHYL-1,3-DIOXANE]-5-YLOXYCARBAMOYL}-ETHANE.
Authors
:
J. G. Ho, P. I. Kitov, E. Paszkiewicz, J. Sadowska, D. R. Bundle, K. K. Ng
Date
:
27 Jun 05 (Deposition) - 26 Jul 05 (Release) - 13 Jul 11 (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
:
Metal Binding Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. G. Ho, P. I. Kitov, E. Paszkiewicz, J. Sadowska, D. R. Bundle, K. K. Ng
Ligand-Assisted Aggregation Of Proteins: Dimerization Of Serum Amyloid P Component By Bivalent Ligands.
J. Biol. Chem. V. 280 31999 2005
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Hetero Components
(2, 15)
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: BIS-1,2-{[(Z)-2-CARBOXY-2-METHYL-1... (CPJa)
2b: BIS-1,2-{[(Z)-2-CARBOXY-2-METHYL-1... (CPJb)
2c: BIS-1,2-{[(Z)-2-CARBOXY-2-METHYL-1... (CPJc)
2d: BIS-1,2-{[(Z)-2-CARBOXY-2-METHYL-1... (CPJd)
2e: BIS-1,2-{[(Z)-2-CARBOXY-2-METHYL-1... (CPJe)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
10
Ligand/Ion
CALCIUM ION
2
CPJ
5
Ligand/Ion
BIS-1,2-{[(Z)-2-CARBOXY-2-METHYL-1,3-DIOXANE]-5-YLOXYCARBAMOYL}-ETHANE
[
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Sites
(15, 15)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:58 , ASN A:59 , GLU A:136 , GLN A:137 , ASP A:138 , CPJ A:610
BINDING SITE FOR RESIDUE CA A 600
02
AC2
SOFTWARE
GLU A:136 , ASP A:138 , GLN A:148 , CPJ A:610 , HOH A:687 , HOH A:688
BINDING SITE FOR RESIDUE CA A 601
03
AC3
SOFTWARE
ASP B:58 , ASN B:59 , GLU B:136 , GLN B:137 , ASP B:138 , CPJ B:611
BINDING SITE FOR RESIDUE CA B 602
04
AC4
SOFTWARE
GLU B:136 , ASP B:138 , GLN B:148 , CPJ B:611 , HOH B:656 , HOH B:657
BINDING SITE FOR RESIDUE CA B 603
05
AC5
SOFTWARE
ASP C:58 , ASN C:59 , GLU C:136 , GLN C:137 , ASP C:138 , CPJ C:612
BINDING SITE FOR RESIDUE CA C 604
06
AC6
SOFTWARE
GLU C:136 , ASP C:138 , GLN C:148 , CPJ C:612 , HOH C:709 , HOH C:710
BINDING SITE FOR RESIDUE CA C 605
07
AC7
SOFTWARE
ASP D:58 , ASN D:59 , GLU D:136 , GLN D:137 , ASP D:138 , CPJ D:614
BINDING SITE FOR RESIDUE CA D 606
08
AC8
SOFTWARE
GLU D:136 , ASP D:138 , GLN D:148 , CPJ D:614 , HOH D:752 , HOH D:753
BINDING SITE FOR RESIDUE CA D 607
09
AC9
SOFTWARE
ASP E:58 , ASN E:59 , GLU E:136 , GLN E:137 , ASP E:138 , CPJ E:613
BINDING SITE FOR RESIDUE CA E 608
10
BC1
SOFTWARE
GLU E:136 , ASP E:138 , GLN E:148 , CPJ E:613 , HOH E:707 , HOH E:708
BINDING SITE FOR RESIDUE CA E 609
11
BC2
SOFTWARE
ASP A:58 , ASN A:59 , GLU A:136 , ASP A:138 , GLN A:148 , CA A:600 , CA A:601
BINDING SITE FOR RESIDUE CPJ A 610
12
BC3
SOFTWARE
ASP B:58 , ASN B:59 , TYR B:74 , GLU B:136 , ASP B:138 , GLN B:148 , CA B:602 , CA B:603
BINDING SITE FOR RESIDUE CPJ B 611
13
BC4
SOFTWARE
ASP C:58 , ASN C:59 , GLU C:136 , ASP C:138 , GLN C:148 , CA C:604 , CA C:605
BINDING SITE FOR RESIDUE CPJ C 612
14
BC5
SOFTWARE
ASP E:58 , ASN E:59 , TYR E:64 , GLU E:136 , ASP E:138 , GLN E:148 , CA E:608 , CA E:609
BINDING SITE FOR RESIDUE CPJ E 613
15
BC6
SOFTWARE
ASP D:58 , ASN D:59 , GLU D:136 , ASP D:138 , GLN D:148 , CA D:606 , CA D:607 , HOH D:756
BINDING SITE FOR RESIDUE CPJ D 614
[
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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...)
;
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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-...)
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All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/1.2
3: Boundary 1.2/-
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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
[
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SCOP Domains
(1, 5)
Info
All SCOP Domains
1a: SCOP_d2a3ya_ (A:)
1b: SCOP_d2a3yb_ (B:)
1c: SCOP_d2a3yc_ (C:)
1d: SCOP_d2a3yd_ (D:)
1e: SCOP_d2a3ye_ (E:)
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Protein Domains
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(
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Organisms
(
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(
)
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
d2a3ya_
A:
1b
d2a3yb_
B:
1c
d2a3yc_
C:
1d
d2a3yd_
D:
1e
d2a3ye_
E:
[
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CATH Domains
(1, 5)
Info
all CATH domains
1a: CATH_2a3yA00 (A:1-204)
1b: CATH_2a3yB00 (B:1-204)
1c: CATH_2a3yC00 (C:1-204)
1d: CATH_2a3yD00 (D:1-204)
1e: CATH_2a3yE00 (E:1-204)
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)
(
)
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
2a3yA00
A:1-204
1b
2a3yB00
B:1-204
1c
2a3yC00
C:1-204
1d
2a3yD00
D:1-204
1e
2a3yE00
E:1-204
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Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Sorry, no Info available
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