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Asym. Unit
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Asym.Unit (371 KB)
Biol.Unit 1 (176 KB)
Biol.Unit 2 (176 KB)
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(1)
Title
:
STRUCTURE OF CPHPC BOUND TO SERUM AMYLOID P COMPONENT
Authors
:
S. E. Kolstoe, A. Purvis, S. P. Wood
Date
:
29 May 12 (Deposition) - 19 Jun 13 (Release) - 22 Oct 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.20
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J
Biol. Unit 1: A,C,E,G,I (1x)
Biol. Unit 2: B,D,F,H,J (1x)
Keywords
:
Sugar Binding Protein, Lectin, Metal-Binding
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. E. Kolstoe, M. C. Jenvey, A. Purvis, M. E. Light, D. Thompson, P. Hughes, M. B. Pepys, S. P. Wood
Interaction Of Serum Amyloid P Component With Hexanoyl Bis(D-Proline) (Cphpc)
Acta Crystallogr. , Sect. D V. 70 2232 2014
[
close entry info
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Hetero Components
(3, 35)
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)
1k: CALCIUM ION (CAk)
1l: CALCIUM ION (CAl)
1m: CALCIUM ION (CAm)
1n: CALCIUM ION (CAn)
1o: CALCIUM ION (CAo)
1p: CALCIUM ION (CAp)
1q: CALCIUM ION (CAq)
1r: CALCIUM ION (CAr)
1s: CALCIUM ION (CAs)
1t: CALCIUM ION (CAt)
2a: (2R)-1-[6-[(2R)-2-CARBOXYPYRROLIDI... (GHEa)
2b: (2R)-1-[6-[(2R)-2-CARBOXYPYRROLIDI... (GHEb)
2c: (2R)-1-[6-[(2R)-2-CARBOXYPYRROLIDI... (GHEc)
2d: (2R)-1-[6-[(2R)-2-CARBOXYPYRROLIDI... (GHEd)
2e: (2R)-1-[6-[(2R)-2-CARBOXYPYRROLIDI... (GHEe)
3a: N-ACETYL-D-GLUCOSAMINE (NAGa)
3b: N-ACETYL-D-GLUCOSAMINE (NAGb)
3c: N-ACETYL-D-GLUCOSAMINE (NAGc)
3d: N-ACETYL-D-GLUCOSAMINE (NAGd)
3e: N-ACETYL-D-GLUCOSAMINE (NAGe)
3f: N-ACETYL-D-GLUCOSAMINE (NAGf)
3g: N-ACETYL-D-GLUCOSAMINE (NAGg)
3h: N-ACETYL-D-GLUCOSAMINE (NAGh)
3i: N-ACETYL-D-GLUCOSAMINE (NAGi)
3j: N-ACETYL-D-GLUCOSAMINE (NAGj)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
20
Ligand/Ion
CALCIUM ION
2
GHE
5
Ligand/Ion
(2R)-1-[6-[(2R)-2-CARBOXYPYRROLIDIN-1-YL]-6-OXIDANYLIDENE-HEXANOYL]PYRROLIDINE-2-CARBOXYLIC ACID
3
NAG
10
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(35, 35)
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)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (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 , GHE B:1207
BINDING SITE FOR RESIDUE CA A1205
02
AC2
SOFTWARE
GLU A:136 , ASP A:138 , GLN A:148 , GHE B:1207
BINDING SITE FOR RESIDUE CA A1206
03
AC3
SOFTWARE
ASP B:58 , ASN B:59 , GLU B:136 , GLN B:137 , ASP B:138 , GHE B:1207
BINDING SITE FOR RESIDUE CA B1205
04
AC4
SOFTWARE
GLU B:136 , ASP B:138 , ASP B:145 , GLN B:148 , GHE B:1207
BINDING SITE FOR RESIDUE CA B1206
05
AC5
SOFTWARE
ASN A:59 , TYR A:64 , TYR A:74 , GLU A:136 , ASP A:138 , GLN A:148 , CA A:1205 , CA A:1206 , ASP B:58 , ASN B:59 , TYR B:64 , GLU B:136 , ASP B:138 , GLN B:148 , CA B:1205 , CA B:1206
BINDING SITE FOR RESIDUE GHE B1207
06
AC6
SOFTWARE
ASP C:58 , ASN C:59 , GLU C:136 , GLN C:137 , ASP C:138 , GHE C:1207
BINDING SITE FOR RESIDUE CA C1205
07
AC7
SOFTWARE
GLU C:136 , ASP C:138 , GLN C:148 , GHE C:1207
BINDING SITE FOR RESIDUE CA C1206
08
AC8
SOFTWARE
ASP C:58 , ASN C:59 , TYR C:64 , TYR C:74 , GLU C:136 , ASP C:138 , GLN C:148 , CA C:1205 , CA C:1206 , ASP D:58 , ASN D:59 , GLU D:136 , ASP D:138 , GLN D:148 , CA D:1205 , CA D:1206
BINDING SITE FOR RESIDUE GHE C1207
09
AC9
SOFTWARE
GHE C:1207 , ASP D:58 , ASN D:59 , GLU D:136 , GLN D:137 , ASP D:138
BINDING SITE FOR RESIDUE CA D1205
10
BC1
SOFTWARE
GHE C:1207 , GLU D:136 , ASP D:138 , GLN D:148
BINDING SITE FOR RESIDUE CA D1206
11
BC2
SOFTWARE
ASP E:58 , ASN E:59 , GLU E:136 , GLN E:137 , ASP E:138 , GHE E:1207
BINDING SITE FOR RESIDUE CA E1205
12
BC3
SOFTWARE
GLU E:136 , ASP E:138 , GLN E:148 , GHE E:1207
BINDING SITE FOR RESIDUE CA E1206
13
BC4
SOFTWARE
ASP E:58 , ASN E:59 , TYR E:64 , TYR E:74 , GLU E:136 , ASP E:138 , GLN E:148 , CA E:1205 , CA E:1206 , ASP F:58 , ASN F:59 , TYR F:74 , GLU F:136 , ASP F:138 , GLN F:148 , CA F:1205 , CA F:1206
BINDING SITE FOR RESIDUE GHE E1207
14
BC5
SOFTWARE
GHE E:1207 , ASP F:58 , ASN F:59 , GLU F:136 , GLN F:137 , ASP F:138
BINDING SITE FOR RESIDUE CA F1205
15
BC6
SOFTWARE
GHE E:1207 , GLU F:136 , ASP F:138 , GLN F:148
BINDING SITE FOR RESIDUE CA F1206
16
BC7
SOFTWARE
ASP G:58 , ASN G:59 , GLU G:136 , GLN G:137 , ASP G:138 , GHE G:1207
BINDING SITE FOR RESIDUE CA G1205
17
BC8
SOFTWARE
GLU G:136 , ASP G:138 , GLN G:148 , GHE G:1207
BINDING SITE FOR RESIDUE CA G1206
18
BC9
SOFTWARE
ASP G:58 , ASN G:59 , LEU G:62 , TYR G:64 , TYR G:74 , GLU G:136 , ASP G:138 , GLN G:148 , CA G:1205 , CA G:1206 , ASP H:58 , ASN H:59 , LEU H:62 , TYR H:74 , GLU H:136 , ASP H:138 , GLN H:148 , CA H:1205 , CA H:1206
BINDING SITE FOR RESIDUE GHE G1207
19
CC1
SOFTWARE
GHE G:1207 , ASP H:58 , ASN H:59 , GLU H:136 , GLN H:137 , ASP H:138
BINDING SITE FOR RESIDUE CA H1205
20
CC2
SOFTWARE
GHE G:1207 , GLU H:136 , ASP H:138 , GLN H:148
BINDING SITE FOR RESIDUE CA H1206
21
CC3
SOFTWARE
ASP I:58 , ASN I:59 , GLU I:136 , GLN I:137 , ASP I:138 , GHE J:1207
BINDING SITE FOR RESIDUE CA I1205
22
CC4
SOFTWARE
GLU I:136 , ASP I:138 , GLN I:148 , GHE J:1207
BINDING SITE FOR RESIDUE CA I1206
23
CC5
SOFTWARE
ASP J:58 , ASN J:59 , GLU J:136 , GLN J:137 , ASP J:138 , GHE J:1207
BINDING SITE FOR RESIDUE CA J1205
24
CC6
SOFTWARE
GLU J:136 , ASP J:138 , GLN J:148 , GHE J:1207
BINDING SITE FOR RESIDUE CA J1206
25
CC7
SOFTWARE
ASP I:58 , ASN I:59 , TYR I:74 , GLU I:136 , ASP I:138 , GLN I:148 , CA I:1205 , CA I:1206 , ASP J:58 , ASN J:59 , LEU J:62 , TYR J:74 , GLU J:136 , ASP J:138 , GLN J:148 , CA J:1205 , CA J:1206
BINDING SITE FOR RESIDUE GHE J1207
26
CC8
SOFTWARE
ASN A:32 , GLU A:99
BINDING SITE FOR MONO-SACCHARIDE NAG A1207 BOUND TO ASN A 32
27
CC9
SOFTWARE
GLN B:31 , ASN B:32 , GLU B:99
BINDING SITE FOR MONO-SACCHARIDE NAG B1208 BOUND TO ASN B 32
28
DC1
SOFTWARE
GLN C:31 , ASN C:32 , GLU C:99
BINDING SITE FOR MONO-SACCHARIDE NAG C1208 BOUND TO ASN C 32
29
DC2
SOFTWARE
GLN D:31 , ASN D:32 , GLU D:99 , SER D:101
BINDING SITE FOR MONO-SACCHARIDE NAG D1207 BOUND TO ASN D 32
30
DC3
SOFTWARE
GLN E:31 , ASN E:32 , GLU E:99 , SER E:101
BINDING SITE FOR MONO-SACCHARIDE NAG E1208 BOUND TO ASN E 32
31
DC4
SOFTWARE
ASN F:32 , GLU F:99 , ASP F:161
BINDING SITE FOR MONO-SACCHARIDE NAG F1207 BOUND TO ASN F 32
32
DC5
SOFTWARE
GLN G:31 , ASN G:32 , GLU G:99
BINDING SITE FOR MONO-SACCHARIDE NAG G1208 BOUND TO ASN G 32
33
DC6
SOFTWARE
GLN H:31 , ASN H:32 , GLU H:99
BINDING SITE FOR MONO-SACCHARIDE NAG H1207 BOUND TO ASN H 32
34
DC7
SOFTWARE
GLN I:31 , ASN I:32 , GLU I:99
BINDING SITE FOR MONO-SACCHARIDE NAG I1207 BOUND TO ASN I 32
35
DC8
SOFTWARE
GLN J:31 , ASN J:32 , GLU J:99
BINDING SITE FOR MONO-SACCHARIDE NAG J1208 BOUND TO ASN J 32
[
close Site info
]
SAPs(SNPs)/Variants
(3, 30)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_035814 (G122S, chain A/B/C/D/E/F/G/H/I/J, )
2: VAR_006054 (E136G, chain A/B/C/D/E/F/G/H/I/J, )
3: VAR_006055 (S139G, chain A/B/C/D/E/F/G/H/I/J, )
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/F/G/H/I/J
G
122
S
2
UniProt
VAR_006054
E
155
G
SAMP_HUMAN
Polymorphism
---
A/B/C/D/E/F/G/H/I/J
E
136
G
3
UniProt
VAR_006055
S
158
G
SAMP_HUMAN
Polymorphism
---
A/B/C/D/E/F/G/H/I/J
S
139
G
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 20)
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
10
A:5-204
B:5-204
C:5-204
D:5-204
E:5-204
F:5-204
G:5-204
H:5-204
I:5-204
J:5-204
2
PTX_1
PS00289
Pentraxin domain signature.
SAMP_HUMAN
112-119
10
A:93-100
B:93-100
C:93-100
D:93-100
E:93-100
F:93-100
G:93-100
H:93-100
I:93-100
J:93-100
[
close PROSITE info
]
Exons
(2, 20)
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
10
A:1-3
B:1-3
C:1-3
D:1-3
E:1-3
F:1-3
G:1-3
H:1-3
I:1-3
J:1-3
3
3
3
3
3
3
3
3
3
3
1.2
ENST00000255040
2
ENSE00000904939
chr1:
159557891-159558655
765
SAMP_HUMAN
22-223
202
10
A:3-204
B:3-204
C:3-204
D:3-204
E:3-204
F:3-204
G:3-204
H:3-204
I:3-204
J:3-204
202
202
202
202
202
202
202
202
202
202
[
close EXON info
]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
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Label:
Sorry, no Info available
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
[
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