PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
4AYU
Asym. Unit
Info
Asym.Unit (208 KB)
Biol.Unit 1 (200 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF N-ACETYL-D-PROLINE BOUND TO SERUM AMYLOID P COMPONENT
Authors
:
P. Hughes, S. E. Kolstoe, S. P. Wood
Date
:
22 Jun 12 (Deposition) - 10 Jul 13 (Release) - 13 Aug 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.50
Chains
:
Asym. Unit : A,B,C,D,E
Biol. Unit 1: A,B,C,D,E (1x)
Keywords
:
Sugar Binding Protein, Lectin
(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
]
Hetero Components
(4, 25)
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: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
3a: N-ACETYL-D-PROLINE (N8Pa)
3b: N-ACETYL-D-PROLINE (N8Pb)
3c: N-ACETYL-D-PROLINE (N8Pc)
3d: N-ACETYL-D-PROLINE (N8Pd)
3e: N-ACETYL-D-PROLINE (N8Pe)
4a: N-ACETYL-D-GLUCOSAMINE (NAGa)
4b: N-ACETYL-D-GLUCOSAMINE (NAGb)
4c: N-ACETYL-D-GLUCOSAMINE (NAGc)
4d: N-ACETYL-D-GLUCOSAMINE (NAGd)
4e: N-ACETYL-D-GLUCOSAMINE (NAGe)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
10
Ligand/Ion
CALCIUM ION
2
GOL
5
Ligand/Ion
GLYCEROL
3
N8P
5
Ligand/Ion
N-ACETYL-D-PROLINE
4
NAG
5
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(25, 25)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:136 , ASP A:138 , GLN A:148 , N8P A:499 , HOH A:2252 , HOH A:2254 , HOH A:2256
BINDING SITE FOR RESIDUE CA A 205
02
AC2
SOFTWARE
ASP A:58 , ASN A:59 , GLU A:136 , GLN A:137 , ASP A:138 , N8P A:499
BINDING SITE FOR RESIDUE CA A 206
03
AC3
SOFTWARE
ASP A:58 , ASN A:59 , LEU A:62 , TYR A:64 , TYR A:74 , GLU A:136 , ASP A:138 , GLN A:148 , CA A:205 , CA A:206 , HOH A:2254 , HOH A:2334
BINDING SITE FOR RESIDUE N8P A 499
04
AC4
SOFTWARE
GLU B:136 , ASP B:138 , GLN B:148 , N8P B:499 , HOH B:2221 , HOH B:2222 , HOH B:2223
BINDING SITE FOR RESIDUE CA B 205
05
AC5
SOFTWARE
ASP B:58 , ASN B:59 , GLU B:136 , GLN B:137 , ASP B:138 , N8P B:499
BINDING SITE FOR RESIDUE CA B 206
06
AC6
SOFTWARE
ASP B:58 , ASN B:59 , LEU B:62 , TYR B:64 , TYR B:74 , GLU B:136 , ASP B:138 , GLN B:148 , CA B:205 , CA B:206 , HOH B:2222 , HOH B:2298
BINDING SITE FOR RESIDUE N8P B 499
07
AC7
SOFTWARE
GLU C:136 , ASP C:138 , GLN C:148 , N8P C:499 , HOH C:2180 , HOH C:2182 , HOH C:2183
BINDING SITE FOR RESIDUE CA C 205
08
AC8
SOFTWARE
ASP C:58 , ASN C:59 , GLU C:136 , GLN C:137 , ASP C:138 , N8P C:499
BINDING SITE FOR RESIDUE CA C 206
09
AC9
SOFTWARE
ASP C:58 , ASN C:59 , LEU C:62 , TYR C:64 , TYR C:74 , GLU C:136 , ASP C:138 , GLN C:148 , CA C:205 , CA C:206 , HOH C:2182
BINDING SITE FOR RESIDUE N8P C 499
10
BC1
SOFTWARE
LYS C:28 , PRO C:29 , GLN C:31 , ASN C:32 , ASP C:161 , NAG C:500
BINDING SITE FOR RESIDUE GOL C1205
11
BC2
SOFTWARE
TYR B:40 , PRO B:91 , TRP B:203 , HOH B:2182 , HOH B:2295 , THR C:112 , PRO C:113
BINDING SITE FOR RESIDUE GOL C1206
12
BC3
SOFTWARE
GLU D:136 , ASP D:138 , GLN D:148 , N8P D:499 , HOH D:2203 , HOH D:2205 , HOH D:2206
BINDING SITE FOR RESIDUE CA D 205
13
BC4
SOFTWARE
ASP D:58 , ASN D:59 , GLU D:136 , GLN D:137 , ASP D:138 , N8P D:499
BINDING SITE FOR RESIDUE CA D 206
14
BC5
SOFTWARE
ASP D:58 , ASN D:59 , LEU D:62 , TYR D:64 , TYR D:74 , GLU D:136 , ASP D:138 , GLN D:148 , CA D:205 , CA D:206 , HOH D:2205
BINDING SITE FOR RESIDUE N8P D 499
15
BC6
SOFTWARE
ASP D:156 , TYR D:158 , GLY D:175 , PRO D:177 , TRP D:185 , HOH D:2020 , HOH D:2079
BINDING SITE FOR RESIDUE GOL D1205
16
BC7
SOFTWARE
ASP D:138 , LYS D:143 , PHE D:144 , HOH D:2206
BINDING SITE FOR RESIDUE GOL D1206
17
BC8
SOFTWARE
GLU E:136 , ASP E:138 , GLN E:148 , N8P E:499 , HOH E:2160 , HOH E:2163
BINDING SITE FOR RESIDUE CA E 205
18
BC9
SOFTWARE
ASP E:58 , ASN E:59 , GLU E:136 , GLN E:137 , ASP E:138 , N8P E:499
BINDING SITE FOR RESIDUE CA E 206
19
CC1
SOFTWARE
ASP E:58 , ASN E:59 , LEU E:62 , TYR E:64 , TYR E:74 , GLU E:136 , ASP E:138 , GLN E:148 , CA E:205 , CA E:206 , HOH E:2225
BINDING SITE FOR RESIDUE N8P E 499
20
CC2
SOFTWARE
PRO E:29 , GLN E:31 , ASN E:32 , ASP E:161
BINDING SITE FOR RESIDUE GOL E1205
21
CC3
SOFTWARE
GLN A:31 , ASN A:32 , GLU A:99 , SER A:101 , HOH A:2084 , HOH A:2278 , HOH A:2335
BINDING SITE FOR MONO-SACCHARIDE NAG A 500 BOUND TO ASN A 32
22
CC4
SOFTWARE
GLN B:31 , ASN B:32 , GLU B:99 , SER B:100 , SER B:101 , HOH B:2077 , HOH B:2078 , HOH B:2299 , HOH B:2300
BINDING SITE FOR MONO-SACCHARIDE NAG B 500 BOUND TO ASN B 32
23
CC5
SOFTWARE
GLN C:31 , ASN C:32 , GLU C:99 , SER C:101 , GOL C:1205 , HOH C:2067
BINDING SITE FOR MONO-SACCHARIDE NAG C 500 BOUND TO ASN C 32
24
CC6
SOFTWARE
GLN D:31 , ASN D:32 , GLU D:99 , HOH D:2074 , HOH D:2266
BINDING SITE FOR MONO-SACCHARIDE NAG D 500 BOUND TO ASN D 32
25
CC7
SOFTWARE
GLN E:31 , ASN E:32 , GLU E:99 , HOH E:2051 , HOH E:2055 , HOH E:2182 , HOH E:2226 , HOH E:2228
BINDING SITE FOR MONO-SACCHARIDE NAG E 500 BOUND TO ASN E 32
[
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)
[
close SNP/Variant info
]
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
[
close PROSITE info
]
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:
Select:
Label:
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_d4ayua_ (A:)
1b: SCOP_d4ayub_ (B:)
1c: SCOP_d4ayuc_ (C:)
1d: SCOP_d4ayud_ (D:)
1e: SCOP_d4ayue_ (E:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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
d4ayua_
A:
1b
d4ayub_
B:
1c
d4ayuc_
C:
1d
d4ayud_
D:
1e
d4ayue_
E:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Chain E
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (208 KB)
Header - Asym.Unit
Biol.Unit 1 (200 KB)
Header - Biol.Unit 1
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
4AYU
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help