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.
3D59
Asym. Unit
Info
Asym.Unit (272 KB)
Biol.Unit 1 (138 KB)
Biol.Unit 2 (133 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN PLASMA PLATELET ACTIVATING FACTOR ACETYLHYDROLASE
Authors
:
U. Samanta, B. J. Bahnson
Date
:
16 May 08 (Deposition) - 09 Sep 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.50
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Plasma Platelet-Activating Factor Acetylhydrolase, Secreted Protein, Alpha/Beta-Hydrolase-Fold, Ldl-Bound; Lipoprotein Associated Phospholipase A2, Lp-Pla2, Group Viia Pla2, Glycoprotein, Hydrolase, Lipid Degradation, Polymorphism, Secreted
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
U. Samanta, B. J. Bahnson
Crystal Structure Of Human Plasma Platelet-Activating Factor Acetylhydrolase: Structural Implication To Lipoprotein Binding And Catalysis.
J. Biol. Chem. V. 283 31617 2008
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 31)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1aa: ACETATE ION (ACTaa)
1ab: ACETATE ION (ACTab)
1ac: ACETATE ION (ACTac)
1b: ACETATE ION (ACTb)
1c: ACETATE ION (ACTc)
1d: ACETATE ION (ACTd)
1e: ACETATE ION (ACTe)
1f: ACETATE ION (ACTf)
1g: ACETATE ION (ACTg)
1h: ACETATE ION (ACTh)
1i: ACETATE ION (ACTi)
1j: ACETATE ION (ACTj)
1k: ACETATE ION (ACTk)
1l: ACETATE ION (ACTl)
1m: ACETATE ION (ACTm)
1n: ACETATE ION (ACTn)
1o: ACETATE ION (ACTo)
1p: ACETATE ION (ACTp)
1q: ACETATE ION (ACTq)
1r: ACETATE ION (ACTr)
1s: ACETATE ION (ACTs)
1t: ACETATE ION (ACTt)
1u: ACETATE ION (ACTu)
1v: ACETATE ION (ACTv)
1w: ACETATE ION (ACTw)
1x: ACETATE ION (ACTx)
1y: ACETATE ION (ACTy)
1z: ACETATE ION (ACTz)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
29
Ligand/Ion
ACETATE ION
2
SO4
2
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(31, 31)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ACT A:15 , LYS A:143 , HIS A:241 , ARG A:264 , HOH A:476 , SER B:308 , ARG B:309 , PRO B:311 , LYS B:339
BINDING SITE FOR RESIDUE ACT A 11
02
AC2
SOFTWARE
SER A:230 , GLN A:231 , SER A:234 , HOH A:494
BINDING SITE FOR RESIDUE ACT A 12
03
AC3
SOFTWARE
ACT A:11 , LYS A:143 , ILE A:262 , ASP A:263 , ARG A:264
BINDING SITE FOR RESIDUE ACT A 15
04
AC4
SOFTWARE
ACT A:28 , SER A:202 , TRP A:203 , TYR B:189 , LYS B:191
BINDING SITE FOR RESIDUE ACT A 16
05
AC5
SOFTWARE
HIS A:74 , ASP A:192 , GLN A:193 , HOH A:662 , HOH A:713
BINDING SITE FOR RESIDUE ACT A 19
06
AC6
SOFTWARE
VAL A:245 , LYS A:246 , ASN A:247 , PHE A:253 , MET A:255 , HOH A:490 , HOH A:495
BINDING SITE FOR RESIDUE ACT A 20
07
AC7
SOFTWARE
PHE A:72 , HOH A:481
BINDING SITE FOR RESIDUE ACT A 22
08
AC8
SOFTWARE
LEU A:124 , THR A:361
BINDING SITE FOR RESIDUE ACT A 24
09
AC9
SOFTWARE
TRP A:298 , TYR A:324 , HOH A:446
BINDING SITE FOR RESIDUE ACT A 25
10
BC1
SOFTWARE
ACT A:16 , LYS A:191 , HOH A:534 , TYR B:189 , LYS B:191 , HOH B:548
BINDING SITE FOR RESIDUE ACT A 28
11
BC2
SOFTWARE
GLU A:305 , SER A:308 , ARG A:309 , ASP B:260
BINDING SITE FOR RESIDUE ACT A 29
12
BC3
SOFTWARE
LYS A:246
BINDING SITE FOR RESIDUE ACT A 30
13
BC4
SOFTWARE
LYS A:394 , HIS A:395
BINDING SITE FOR RESIDUE ACT A 32
14
BC5
SOFTWARE
PRO A:57 , ARG A:58 , ASN A:378 , HOH A:548 , HOH A:566 , HOH A:711
BINDING SITE FOR RESIDUE ACT A 33
15
BC6
SOFTWARE
ASN A:378 , VAL A:379 , ASP A:382 , HOH A:510
BINDING SITE FOR RESIDUE ACT A 35
16
BC7
SOFTWARE
ARG A:182 , HOH A:555 , HOH A:700
BINDING SITE FOR RESIDUE ACT A 36
17
BC8
SOFTWARE
ASP A:338 , GLU A:410 , ASP A:412 , PRO A:418 , HOH A:542 , HOH A:635 , HOH A:710
BINDING SITE FOR RESIDUE ACT A 39
18
BC9
SOFTWARE
LYS A:101 , LYS A:201 , ARG B:182 , ARG B:207 , HOH B:471 , HOH B:482 , HOH B:490 , HOH B:496
BINDING SITE FOR RESIDUE SO4 B 1
19
CC1
SOFTWARE
ASP A:89 , ASN A:90 , ASN B:100 , LYS B:101 , HOH B:521 , HOH B:634
BINDING SITE FOR RESIDUE SO4 B 2
20
CC2
SOFTWARE
TRP B:134 , LEU B:251 , HOH B:518
BINDING SITE FOR RESIDUE ACT B 13
21
CC3
SOFTWARE
TYR B:321 , PHE B:322 , VAL B:350 , HIS B:351 , HOH B:449
BINDING SITE FOR RESIDUE ACT B 14
22
CC4
SOFTWARE
SER B:230 , GLN B:231 , SER B:234
BINDING SITE FOR RESIDUE ACT B 17
23
CC5
SOFTWARE
LYS B:266 , LEU B:398 , HIS B:399
BINDING SITE FOR RESIDUE ACT B 18
24
CC6
SOFTWARE
TRP B:298 , PHE B:300 , TYR B:324 , HOH B:441
BINDING SITE FOR RESIDUE ACT B 21
25
CC7
SOFTWARE
LEU B:107 , PHE B:357
BINDING SITE FOR RESIDUE ACT B 23
26
CC8
SOFTWARE
LYS A:259 , HOH A:679 , ARG B:309
BINDING SITE FOR RESIDUE ACT B 26
27
CC9
SOFTWARE
HIS B:74 , ASP B:192 , GLN B:193
BINDING SITE FOR RESIDUE ACT B 27
28
DC1
SOFTWARE
HOH B:593
BINDING SITE FOR RESIDUE ACT B 31
29
DC2
SOFTWARE
PHE B:110
BINDING SITE FOR RESIDUE ACT B 34
30
DC3
SOFTWARE
LYS A:370 , HOH A:620 , ILE B:329 , HOH B:639
BINDING SITE FOR RESIDUE ACT B 37
31
DC4
SOFTWARE
PRO B:140 , ASP B:412 , HOH B:594
BINDING SITE FOR RESIDUE ACT B 38
[
close Site info
]
SAPs(SNPs)/Variants
(6, 12)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_011583 (R92H, chain A/B, )
2: VAR_047971 (K191N, chain A/B, )
3: VAR_011584 (I198T, chain A/B, )
4: VAR_004268 (V279F, chain A/B, )
5: VAR_011585 (Q281R, chain A/B, )
6: VAR_011586 (V379A, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_011583
R
92
H
PAFA_HUMAN
Polymorphism
1805017
A/B
R
92
H
2
UniProt
VAR_047971
K
191
N
PAFA_HUMAN
Polymorphism
45454695
A/B
K
191
N
3
UniProt
VAR_011584
I
198
T
PAFA_HUMAN
Polymorphism
1805018
A/B
I
198
T
4
UniProt
VAR_004268
V
279
F
PAFA_HUMAN
Disease (PAFAD)
16874954
A/B
V
279
F
5
UniProt
VAR_011585
Q
281
R
PAFA_HUMAN
Disease (PAFAD)
---
A/B
Q
281
R
6
UniProt
VAR_011586
V
379
A
PAFA_HUMAN
Polymorphism
1051931
A/B
V
379
A
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: LIPASE_SER (A:267-276,B:267-276)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
LIPASE_SER
PS00120
Lipases, serine active site.
PAFA_HUMAN
267-276
2
A:267-276
B:267-276
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
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.
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
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
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 (272 KB)
Header - Asym.Unit
Biol.Unit 1 (138 KB)
Header - Biol.Unit 1
Biol.Unit 2 (133 KB)
Header - Biol.Unit 2
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
3D59
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help