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.
1LGN
Asym. Unit
Info
Asym.Unit (176 KB)
Biol.Unit 1 (170 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
DECAMERIC DAMP COMPLEX OF HUMAN SERUM AMYLOID P COMPONENT
Authors
:
E. Hohenester, M. B. Pepys, S. P. Wood
Date
:
04 Dec 96 (Deposition) - 24 Dec 97 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B,C,D,E
Biol. Unit 1: A,B,C,D,E (1x)
Keywords
:
Serum Protein, Amyloidosis, Drug Design, Nucleotide
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. Hohenester, W. L. Hutchinson, M. B. Pepys, S. P. Wood
Crystal Structure Of A Decameric Complex Of Human Serum Amyloid P Component With Bound Damp.
J. Mol. Biol. V. 269 570 1997
(for further references see the
PDB file header
)
[
close entry info
]
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: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE (DAa)
2b: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE (DAb)
2c: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE (DAc)
2d: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE (DAd)
2e: 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE (DAe)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
10
Ligand/Ion
CALCIUM ION
2
DA
5
Ligand/Ion
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
[
close Hetero Component info
]
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:
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 , DA A:401
BINDING SITE FOR RESIDUE CA A 301
02
AC2
SOFTWARE
GLU A:136 , ASP A:138 , GLN A:148 , DA A:401
BINDING SITE FOR RESIDUE CA A 302
03
AC3
SOFTWARE
ASP B:58 , ASN B:59 , GLU B:136 , GLN B:137 , ASP B:138 , DA B:401
BINDING SITE FOR RESIDUE CA B 301
04
AC4
SOFTWARE
GLU B:136 , ASP B:138 , ASP B:145 , GLN B:148 , DA B:401
BINDING SITE FOR RESIDUE CA B 302
05
AC5
SOFTWARE
ASP C:58 , ASN C:59 , GLU C:136 , GLN C:137 , ASP C:138 , DA C:401
BINDING SITE FOR RESIDUE CA C 301
06
AC6
SOFTWARE
GLU C:136 , ASP C:138 , GLN C:148 , DA C:401
BINDING SITE FOR RESIDUE CA C 302
07
AC7
SOFTWARE
ASP D:58 , ASN D:59 , GLU D:136 , GLN D:137 , ASP D:138 , DA D:401
BINDING SITE FOR RESIDUE CA D 301
08
AC8
SOFTWARE
GLU D:136 , ASP D:138 , ASP D:145 , GLN D:148 , DA D:401
BINDING SITE FOR RESIDUE CA D 302
09
AC9
SOFTWARE
ASP E:58 , ASN E:59 , GLU E:136 , GLN E:137 , ASP E:138 , DA E:401
BINDING SITE FOR RESIDUE CA E 301
10
BC1
SOFTWARE
GLU E:136 , ASP E:138 , ASP E:145 , GLN E:148 , DA E:401
BINDING SITE FOR RESIDUE CA E 302
11
BC2
SOFTWARE
ASP A:58 , ASN A:59 , TYR A:64 , TYR A:74 , GLU A:136 , ASP A:138 , ASP A:145 , SER A:147 , GLN A:148 , CA A:301 , CA A:302 , DA E:401
BINDING SITE FOR RESIDUE DA A 401
12
BC3
SOFTWARE
ASP B:58 , ASN B:59 , TYR B:64 , TYR B:74 , GLU B:136 , ASP B:138 , SER B:147 , GLN B:148 , CA B:301 , CA B:302 , DA D:401
BINDING SITE FOR RESIDUE DA B 401
13
BC4
SOFTWARE
ASP C:58 , ASN C:59 , TYR C:64 , TYR C:74 , GLU C:136 , ASP C:138 , SER C:147 , GLN C:148 , CA C:301 , CA C:302
BINDING SITE FOR RESIDUE DA C 401
14
BC5
SOFTWARE
DA B:401 , ASP D:58 , ASN D:59 , TYR D:64 , TYR D:74 , GLU D:136 , ASP D:138 , ASP D:145 , SER D:147 , GLN D:148 , CA D:301 , CA D:302
BINDING SITE FOR RESIDUE DA D 401
15
BC6
SOFTWARE
DA A:401 , ASP E:58 , ASN E:59 , TYR E:64 , TYR E:74 , GLU E:136 , ASP E:138 , SER E:147 , GLN E:148 , CA E:301 , CA E:302
BINDING SITE FOR RESIDUE DA E 401
[
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_d1lgna_ (A:)
1b: SCOP_d1lgnb_ (B:)
1c: SCOP_d1lgnc_ (C:)
1d: SCOP_d1lgnd_ (D:)
1e: SCOP_d1lgne_ (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
d1lgna_
A:
1b
d1lgnb_
B:
1c
d1lgnc_
C:
1d
d1lgnd_
D:
1e
d1lgne_
E:
[
close SCOP info
]
CATH Domains
(1, 5)
Info
all CATH domains
1a: CATH_1lgnA00 (A:1-204)
1b: CATH_1lgnB00 (B:1-204)
1c: CATH_1lgnC00 (C:1-204)
1d: CATH_1lgnD00 (D:1-204)
1e: CATH_1lgnE00 (E:1-204)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
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
1lgnA00
A:1-204
1b
1lgnB00
B:1-204
1c
1lgnC00
C:1-204
1d
1lgnD00
D:1-204
1e
1lgnE00
E:1-204
[
close CATH info
]
Pfam Domains
(1, 5)
Info
all PFAM domains
1a: PFAM_Pentaxin_1lgnE01 (E:7-200)
1b: PFAM_Pentaxin_1lgnE02 (E:7-200)
1c: PFAM_Pentaxin_1lgnE03 (E:7-200)
1d: PFAM_Pentaxin_1lgnE04 (E:7-200)
1e: PFAM_Pentaxin_1lgnE05 (E:7-200)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Concanavalin
(293)
Family
:
Pentaxin
(6)
Homo sapiens (Human)
(6)
1a
Pentaxin-1lgnE01
E:7-200
1b
Pentaxin-1lgnE02
E:7-200
1c
Pentaxin-1lgnE03
E:7-200
1d
Pentaxin-1lgnE04
E:7-200
1e
Pentaxin-1lgnE05
E:7-200
[
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 (176 KB)
Header - Asym.Unit
Biol.Unit 1 (170 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
1LGN
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
