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1GYK
Asym. Unit
Info
Asym.Unit (175 KB)
Biol.Unit 1 (168 KB)
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(1)
Title
:
SERUM AMYLOID P COMPONENT CO-CRYSTALLISED WITH MOBDG AT NEUTRAL PH
Authors
:
D. Thompson, M. B. Pepys, I. Tickle, S. P. Wood
Date
:
25 Apr 02 (Deposition) - 22 May 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D,E
Biol. Unit 1: A,B,C,D,E (1x)
Keywords
:
Pentraxin, Amyloid Lectin, Glycoprotein, Plasma, Polymorphism
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. Thompson, M. B. Pepys, I. Tickle, S. P. Wood
The Structures Of Crystalline Complexes Of Human Serum Amyloid P Component With Its Carbohydrate Ligand, The Cyclic Pyruvate Acetal Of Galactose
J. Mol. Biol. V. 320 1081 2002
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close entry info
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Hetero Components
(2, 13)
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)
2a: METHYL 4,6-O-[(1R)-1-CARBOXYETHYLI... (CDGa)
2b: METHYL 4,6-O-[(1R)-1-CARBOXYETHYLI... (CDGb)
2c: METHYL 4,6-O-[(1R)-1-CARBOXYETHYLI... (CDGc)
2d: METHYL 4,6-O-[(1R)-1-CARBOXYETHYLI... (CDGd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
9
Ligand/Ion
CALCIUM ION
2
CDG
4
Ligand/Ion
METHYL 4,6-O-[(1R)-1-CARBOXYETHYLIDENE]-BETA-D-GALACTOPYRANOSIDE
[
close Hetero Component info
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Sites
(13, 13)
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)
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 , CDG A:1207
BINDING SITE FOR RESIDUE CA A1205
02
AC2
SOFTWARE
GLU A:136 , ASP A:138 , GLN A:148 , CDG A: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 , CDG B:1207
BINDING SITE FOR RESIDUE CA B1205
04
AC4
SOFTWARE
GLU B:136 , ASP B:138 , GLN B:148 , CDG B:1207
BINDING SITE FOR RESIDUE CA B1206
05
AC5
SOFTWARE
ASP C:58 , ASN C:59 , GLU C:136 , GLN C:137 , ASP C:138 , CDG C:1207
BINDING SITE FOR RESIDUE CA C1205
06
AC6
SOFTWARE
GLU C:136 , ASP C:138 , GLN C:148 , CDG C:1207
BINDING SITE FOR RESIDUE CA C1206
07
AC7
SOFTWARE
ASP D:58 , ASN D:59 , GLU D:136 , GLN D:137 , ASP D:138 , CDG D:1207
BINDING SITE FOR RESIDUE CA D1205
08
AC8
SOFTWARE
GLU D:136 , ASP D:138 , GLN D:148 , CDG D:1207
BINDING SITE FOR RESIDUE CA D1206
09
AC9
SOFTWARE
ASP E:58 , ASN E:59 , GLU E:136 , GLN E:137 , ASP E:138
BINDING SITE FOR RESIDUE CA E1205
10
BC1
SOFTWARE
ASP A:58 , ASN A:59 , GLU A:136 , ASP A:138 , GLN A:148 , CA A:1205 , CA A:1206
BINDING SITE FOR RESIDUE CDG A1207
11
BC2
SOFTWARE
ASP B:58 , ASN B:59 , GLU B:136 , ASP B:138 , GLN B:148 , CA B:1205 , CA B:1206
BINDING SITE FOR RESIDUE CDG B1207
12
BC3
SOFTWARE
ASP C:58 , ASN C:59 , GLU C:136 , ASP C:138 , GLN C:148 , CA C:1205 , CA C:1206
BINDING SITE FOR RESIDUE CDG C1207
13
BC4
SOFTWARE
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 CDG D1207
[
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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...)
;
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:
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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_d1gyka_ (A:)
1b: SCOP_d1gykb_ (B:)
1c: SCOP_d1gykc_ (C:)
1d: SCOP_d1gykd_ (D:)
1e: SCOP_d1gyke_ (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
d1gyka_
A:
1b
d1gykb_
B:
1c
d1gykc_
C:
1d
d1gykd_
D:
1e
d1gyke_
E:
[
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CATH Domains
(1, 5)
Info
all CATH domains
1a: CATH_1gykA00 (A:1-204)
1b: CATH_1gykB00 (B:1-204)
1c: CATH_1gykC00 (C:1-204)
1d: CATH_1gykD00 (D:1-204)
1e: CATH_1gykE00 (E:1-204)
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Topologies
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(
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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
1gykA00
A:1-204
1b
1gykB00
B:1-204
1c
1gykC00
C:1-204
1d
1gykD00
D:1-204
1e
1gykE00
E:1-204
[
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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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Chain E
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