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2A3W
Biol. Unit 3
Info
Asym.Unit (734 KB)
Biol.Unit 1 (368 KB)
Biol.Unit 2 (360 KB)
Biol.Unit 3 (187 KB)
Biol.Unit 4 (194 KB)
Biol.Unit 5 (188 KB)
Biol.Unit 6 (187 KB)
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(1)
Title
:
DECAMERIC STRUCTURE OF HUMAN SERUM AMYLOID P-COMPONENT BOUND TO BIS-1, 2-{[(Z)-2-CARBOXY-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
:
2.20
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J (1x)
Biol. Unit 2: K,L,M,N,O,P,Q,R,S,T (1x)
Biol. Unit 3: K,L,M,N,O (1x)
Biol. Unit 4: A,B,C,D,E (1x)
Biol. Unit 5: F,G,H,I,J (1x)
Biol. Unit 6: P,Q,R,S,T (1x)
Keywords
:
Multivalent Ligand Complex, 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
[
close entry info
]
Hetero Components
(1, 3)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1aa: CALCIUM ION (CAaa)
1ab: CALCIUM ION (CAab)
1ac: CALCIUM ION (CAac)
1ad: CALCIUM ION (CAad)
1ae: CALCIUM ION (CAae)
1af: CALCIUM ION (CAaf)
1ag: CALCIUM ION (CAag)
1ah: CALCIUM ION (CAah)
1ai: CALCIUM ION (CAai)
1aj: CALCIUM ION (CAaj)
1ak: CALCIUM ION (CAak)
1al: CALCIUM ION (CAal)
1am: CALCIUM ION (CAam)
1an: CALCIUM ION (CAan)
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)
1u: CALCIUM ION (CAu)
1v: CALCIUM ION (CAv)
1w: CALCIUM ION (CAw)
1x: CALCIUM ION (CAx)
1y: CALCIUM ION (CAy)
1z: CALCIUM ION (CAz)
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)
2f: BIS-1,2-{[(Z)-2-CARBOXY-2-METHYL-1... (CPJf)
2g: BIS-1,2-{[(Z)-2-CARBOXY-2-METHYL-1... (CPJg)
2h: BIS-1,2-{[(Z)-2-CARBOXY-2-METHYL-1... (CPJh)
2i: BIS-1,2-{[(Z)-2-CARBOXY-2-METHYL-1... (CPJi)
2j: BIS-1,2-{[(Z)-2-CARBOXY-2-METHYL-1... (CPJj)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
CPJ
3
Ligand/Ion
BIS-1,2-{[(Z)-2-CARBOXY-2-METHYL-1,3-DIOXANE]-5-YLOXYCARBAMOYL}-ETHANE
[
close Hetero Component info
]
Sites
(21, 21)
Info
All Sites
01: CC3 (SOFTWARE)
02: CC4 (SOFTWARE)
03: CC5 (SOFTWARE)
04: CC6 (SOFTWARE)
05: CC7 (SOFTWARE)
06: CC8 (SOFTWARE)
07: CC9 (SOFTWARE)
08: DC1 (SOFTWARE)
09: DC2 (SOFTWARE)
10: DC3 (SOFTWARE)
11: DC8 (SOFTWARE)
12: DC9 (SOFTWARE)
13: EC1 (SOFTWARE)
14: EC2 (SOFTWARE)
15: EC3 (SOFTWARE)
16: EC4 (SOFTWARE)
17: FC1 (SOFTWARE)
18: FC2 (SOFTWARE)
19: FC3 (SOFTWARE)
20: FC4 (SOFTWARE)
21: FC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
CC3
SOFTWARE
ASP K:58 , ASN K:59 , GLU K:136 , GLN K:137 , ASP K:138 , CA K:322 , CPJ P:346
BINDING SITE FOR RESIDUE CA K 321
02
CC4
SOFTWARE
GLU K:136 , ASP K:138 , GLN K:148 , CA K:321 , HOH K:667 , CPJ P:346 , HOH P:666
BINDING SITE FOR RESIDUE CA K 322
03
CC5
SOFTWARE
GLU L:136 , ASP L:138 , GLN L:148 , CPJ L:347 , HOH L:668 , HOH L:669
BINDING SITE FOR RESIDUE CA L 323
04
CC6
SOFTWARE
ASP L:58 , ASN L:59 , GLU L:136 , GLN L:137 , ASP L:138 , CPJ L:347
BINDING SITE FOR RESIDUE CA L 324
05
CC7
SOFTWARE
ASP M:58 , ASN M:59 , GLU M:136 , GLN M:137 , ASP M:138 , CPJ M:348
BINDING SITE FOR RESIDUE CA M 325
06
CC8
SOFTWARE
GLU M:136 , ASP M:138 , GLN M:148 , CPJ M:348 , HOH M:670 , HOH M:671
BINDING SITE FOR RESIDUE CA M 326
07
CC9
SOFTWARE
ASP N:58 , ASN N:59 , GLU N:136 , GLN N:137 , ASP N:138 , CPJ N:349
BINDING SITE FOR RESIDUE CA N 327
08
DC1
SOFTWARE
GLU N:136 , ASP N:138 , GLN N:148 , CPJ N:349 , HOH N:672 , HOH N:673
BINDING SITE FOR RESIDUE CA N 328
09
DC2
SOFTWARE
ASP O:58 , ASN O:59 , GLU O:136 , GLN O:137 , ASP O:138 , CPJ Q:350
BINDING SITE FOR RESIDUE CA O 329
10
DC3
SOFTWARE
GLU O:136 , ASP O:138 , GLN O:148 , HOH O:674 , HOH O:675 , CPJ Q:350
BINDING SITE FOR RESIDUE CA O 330
11
DC8
SOFTWARE
CPJ N:349 , ASP R:58 , ASN R:59 , GLU R:136 , GLN R:137 , ASP R:138
BINDING SITE FOR RESIDUE CA R 335
12
DC9
SOFTWARE
CPJ N:349 , GLU R:136 , ASP R:138 , GLN R:148 , HOH R:680
BINDING SITE FOR RESIDUE CA R 336
13
EC1
SOFTWARE
CPJ M:348 , ASP S:58 , ASN S:59 , GLU S:136 , GLN S:137 , ASP S:138
BINDING SITE FOR RESIDUE CA S 337
14
EC2
SOFTWARE
CPJ M:348 , GLU S:136 , ASP S:138 , GLN S:148 , HOH S:681 , HOH S:682
BINDING SITE FOR RESIDUE CA S 338
15
EC3
SOFTWARE
CPJ L:347 , ASP T:58 , ASN T:59 , GLU T:136 , GLN T:137 , ASP T:138
BINDING SITE FOR RESIDUE CA T 339
16
EC4
SOFTWARE
CPJ L:347 , GLU T:136 , ASP T:138 , GLN T:148 , HOH T:683 , HOH T:684
BINDING SITE FOR RESIDUE CA T 340
17
FC1
SOFTWARE
ASP K:58 , ASN K:59 , LEU K:62 , TYR K:74 , GLU K:136 , ASP K:138 , GLN K:148 , CA K:321 , CA K:322 , ASP P:58 , ASN P:59 , LEU P:62 , TYR P:74 , GLU P:136 , ASP P:138 , GLN P:148 , CA P:331 , CA P:332 , HOH P:666 , HOH P:2706
BINDING SITE FOR RESIDUE CPJ P 346
18
FC2
SOFTWARE
ASP L:58 , ASN L:59 , LEU L:62 , TYR L:74 , GLU L:136 , ASP L:138 , GLN L:148 , CA L:323 , CA L:324 , HOH L:1274 , HOH L:2355 , ASP T:58 , ASN T:59 , LEU T:62 , TYR T:74 , GLU T:136 , ASP T:138 , GLN T:148 , CA T:339 , CA T:340 , HOH T:684
BINDING SITE FOR RESIDUE CPJ L 347
19
FC3
SOFTWARE
ASP M:58 , ASN M:59 , LEU M:62 , TYR M:64 , TYR M:74 , GLU M:136 , ASP M:138 , GLN M:148 , CA M:325 , CA M:326 , HOH M:1859 , HOH M:3370 , ASP S:58 , ASN S:59 , LEU S:62 , TYR S:74 , GLU S:136 , ASP S:138 , GLN S:148 , CA S:337 , CA S:338 , HOH S:682
BINDING SITE FOR RESIDUE CPJ M 348
20
FC4
SOFTWARE
ASP N:58 , ASN N:59 , LEU N:62 , TYR N:74 , GLU N:136 , ASP N:138 , GLN N:148 , CA N:327 , CA N:328 , HOH N:673 , ASP R:58 , ASN R:59 , LEU R:62 , TYR R:74 , GLU R:136 , ASP R:138 , GLN R:148 , CA R:335 , CA R:336
BINDING SITE FOR RESIDUE CPJ N 349
21
FC5
SOFTWARE
ASP O:58 , ASN O:59 , LEU O:62 , TYR O:74 , GLU O:136 , ASP O:138 , GLN O:148 , CA O:329 , CA O:330 , ASP Q:58 , ASN Q:59 , LEU Q:62 , TYR Q:74 , GLU Q:136 , ASP Q:138 , GLN Q:148 , CA Q:333 , CA Q:334 , HOH Q:1694
BINDING SITE FOR RESIDUE CPJ Q 350
[
close Site info
]
SAPs(SNPs)/Variants
(3, 15)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_035814 (G122S, chain K/L/M/N/O, )
2: VAR_006054 (E136G, chain K/L/M/N/O, )
3: VAR_006055 (S139G, chain K/L/M/N/O, )
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
---
K/L/M/N/O
G
122
S
2
UniProt
VAR_006054
E
155
G
SAMP_HUMAN
Polymorphism
---
K/L/M/N/O
E
136
G
3
UniProt
VAR_006055
S
158
G
SAMP_HUMAN
Polymorphism
---
K/L/M/N/O
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 (K:5-204,L:5-204,M:5-204,N:5-204,O:...)
2: PTX_1 (K:93-100,L:93-100,M:93-100,N: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
-
-
-
-
-
-
-
-
-
-
K:5-204
L:5-204
M:5-204
N:5-204
O:5-204
-
-
-
-
-
2
PTX_1
PS00289
Pentraxin domain signature.
SAMP_HUMAN
112-119
5
-
-
-
-
-
-
-
-
-
-
K:93-100
L:93-100
M:93-100
N:93-100
O:93-100
-
-
-
-
-
[
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]
Exons
(0, 0)
Info
All Exons
View:
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All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 20)
Info
All SCOP Domains
1a: SCOP_d2a3wa_ (A:)
1b: SCOP_d2a3wb_ (B:)
1c: SCOP_d2a3wc_ (C:)
1d: SCOP_d2a3wd_ (D:)
1e: SCOP_d2a3we_ (E:)
1f: SCOP_d2a3wf_ (F:)
1g: SCOP_d2a3wg_ (G:)
1h: SCOP_d2a3wh_ (H:)
1i: SCOP_d2a3wi_ (I:)
1j: SCOP_d2a3wj_ (J:)
1k: SCOP_d2a3wk_ (K:)
1l: SCOP_d2a3wl_ (L:)
1m: SCOP_d2a3wm_ (M:)
1n: SCOP_d2a3wn_ (N:)
1o: SCOP_d2a3wo_ (O:)
1p: SCOP_d2a3wp_ (P:)
1q: SCOP_d2a3wq_ (Q:)
1r: SCOP_d2a3wr_ (R:)
1s: SCOP_d2a3ws_ (S:)
1t: SCOP_d2a3wt_ (T:)
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)
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)
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(
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(
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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
d2a3wa_
A:
1b
d2a3wb_
B:
1c
d2a3wc_
C:
1d
d2a3wd_
D:
1e
d2a3we_
E:
1f
d2a3wf_
F:
1g
d2a3wg_
G:
1h
d2a3wh_
H:
1i
d2a3wi_
I:
1j
d2a3wj_
J:
1k
d2a3wk_
K:
1l
d2a3wl_
L:
1m
d2a3wm_
M:
1n
d2a3wn_
N:
1o
d2a3wo_
O:
1p
d2a3wp_
P:
1q
d2a3wq_
Q:
1r
d2a3wr_
R:
1s
d2a3ws_
S:
1t
d2a3wt_
T:
[
close SCOP info
]
CATH Domains
(1, 20)
Info
all CATH domains
1a: CATH_2a3wA00 (A:1-204)
1b: CATH_2a3wB00 (B:1-204)
1c: CATH_2a3wC00 (C:1-204)
1d: CATH_2a3wD00 (D:1-204)
1e: CATH_2a3wE00 (E:1-204)
1f: CATH_2a3wF00 (F:1-204)
1g: CATH_2a3wG00 (G:1-204)
1h: CATH_2a3wH00 (H:1-204)
1i: CATH_2a3wI00 (I:1-204)
1j: CATH_2a3wJ00 (J:1-204)
1k: CATH_2a3wK00 (K:1-204)
1l: CATH_2a3wL00 (L:1-204)
1m: CATH_2a3wM00 (M:1-204)
1n: CATH_2a3wN00 (N:1-204)
1o: CATH_2a3wO00 (O:1-204)
1p: CATH_2a3wP00 (P:1-204)
1q: CATH_2a3wQ00 (Q:1-204)
1r: CATH_2a3wR00 (R:1-204)
1s: CATH_2a3wS00 (S:1-204)
1t: CATH_2a3wT00 (T:1-204)
View:
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Topologies
(
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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
2a3wA00
A:1-204
1b
2a3wB00
B:1-204
1c
2a3wC00
C:1-204
1d
2a3wD00
D:1-204
1e
2a3wE00
E:1-204
1f
2a3wF00
F:1-204
1g
2a3wG00
G:1-204
1h
2a3wH00
H:1-204
1i
2a3wI00
I:1-204
1j
2a3wJ00
J:1-204
1k
2a3wK00
K:1-204
1l
2a3wL00
L:1-204
1m
2a3wM00
M:1-204
1n
2a3wN00
N:1-204
1o
2a3wO00
O:1-204
1p
2a3wP00
P:1-204
1q
2a3wQ00
Q:1-204
1r
2a3wR00
R:1-204
1s
2a3wS00
S:1-204
1t
2a3wT00
T:1-204
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
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