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.
1FDP
Asym. Unit
Info
Asym.Unit (143 KB)
Biol.Unit 1 (40 KB)
Biol.Unit 2 (37 KB)
Biol.Unit 3 (36 KB)
Biol.Unit 4 (37 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
PROENZYME OF HUMAN COMPLEMENT FACTOR D, RECOMBINANT PROFACTOR D
Authors
:
H. Jing, K. J. Macon, D. Moore, L. J. Delucas, J. E. Volanakis, S. V. L. Nar
Date
:
03 Dec 98 (Deposition) - 03 Dec 99 (Release) - 07 Dec 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
Serine Protease, Complement, Factor D, Profactor D, Zymogen, Proenzyme, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Jing, K. J. Macon, D. Moore, L. J. Delucas, J. E. Volanakis, S. V. Narayana
Structural Basis Of Profactor D Activation: From A Highly Flexible Zymogen To A Novel Self-Inhibited Serine Protease, Complement Factor D.
Embo J. V. 18 804 1999
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(0, 0)
Info
All Hetero Components
View:
Select:
Label:
Sorry, no Info available
[
close Hetero component info
]
Sites
(4, 4)
Info
All Sites
1: TRA (AUTHOR)
2: TRB (AUTHOR)
3: TRC (AUTHOR)
4: TRD (AUTHOR)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
TRA
AUTHOR
HIS A:57 , ASP A:102 , SER A:195
CATALYTIC TRIAD
2
TRB
AUTHOR
HIS B:57 , ASP B:102 , SER B:195
CATALYTIC TRIAD
3
TRC
AUTHOR
HIS C:57 , ASP C:102 , SER C:195
CATALYTIC TRIAD
4
TRD
AUTHOR
HIS D:57 , ASP D:102 , SER D:195
CATALYTIC TRIAD
[
close Site info
]
SAPs(SNPs)/Variants
(3, 12)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_034866 (V200G, chain A/B/C/D, )
2: VAR_034867 (C201R, chain A/B/C/D, )
3: VAR_034868 (I238M, chain A/B/C/D, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_034866
V
213
G
CFAD_HUMAN
Disease (CFDD)
---
A/B/C/D
V
200
G
2
UniProt
VAR_034867
C
214
R
CFAD_HUMAN
Disease (CFDD)
---
A/B/C/D
C
201
R
3
UniProt
VAR_034868
I
248
M
CFAD_HUMAN
Polymorphism
2230216
A/B/C/D
I
238
M
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 9)
Info
All PROSITE Patterns/Profiles
1: TRYPSIN_DOM (A:16-243)
2: TRYPSIN_HIS (A:53-58,B:53-58,C:53-58,D:53-58)
3: TRYPSIN_SER (A:189-200,B:193-200,C:194-200,D:19...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TRYPSIN_DOM
PS50240
Serine proteases, trypsin domain profile.
CFAD_HUMAN
26-253
1
A:16-243
2
TRYPSIN_HIS
PS00134
Serine proteases, trypsin family, histidine active site.
CFAD_HUMAN
62-67
4
A:53-58
B:53-58
C:53-58
D:53-58
3
TRYPSIN_SER
PS00135
Serine proteases, trypsin family, serine active site.
CFAD_HUMAN
202-213
4
A:189-200
B:193-200
C:194-200
D:194-200
[
close PROSITE info
]
Exons
(4, 16)
Info
All Exons
Exon 1.2 (A:16-61A (gaps) | B:22-61A (gaps) ...)
Exon 1.3 (A:61A-107 | B:61A-107 | C:61A-107 ...)
Exon 1.4 (A:108-192 (gaps) | B:108-186 (gaps...)
Exon 1.5 (A:193-243 (gaps) | B:193-243 (gaps...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.1/1.2
2: Boundary 1.2/1.3
3: Boundary 1.3/1.4
4: Boundary 1.4/1.5
5: Boundary 1.5/-
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
ENST00000327726
1
ENSE00001231576
chr19:
859665-859744
80
CFAD_HUMAN
1-19
19
0
-
-
1.2
ENST00000327726
2
ENSE00001231561
chr19:
860617-860773
157
CFAD_HUMAN
19-71
53
4
A:16-61A (gaps)
B:22-61A (gaps)
C:22-61A (gaps)
D:22-61A (gaps)
47
41
41
41
1.3
ENST00000327726
3
ENSE00001231555
chr19:
860861-861005
145
CFAD_HUMAN
71-119
49
4
A:61A-107
B:61A-107
C:61A-107
D:61A-107
49
49
49
49
1.4
ENST00000327726
4
ENSE00001374327
chr19:
861699-861956
258
CFAD_HUMAN
120-205
86
4
A:108-192 (gaps)
B:108-186 (gaps)
C:108-186 (gaps)
D:108-186 (gaps)
89
83
83
83
1.5
ENST00000327726
5
ENSE00001354943
chr19:
863092-863606
515
CFAD_HUMAN
206-253
48
4
A:193-243 (gaps)
B:193-243 (gaps)
C:194-243 (gaps)
D:194-243 (gaps)
52
52
51
51
[
close EXON info
]
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d1fdpa_ (A:)
1b: SCOP_d1fdpb_ (B:)
1c: SCOP_d1fdpc_ (C:)
1d: SCOP_d1fdpd_ (D:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Trypsin-like serine proteases
(1752)
Superfamily
:
Trypsin-like serine proteases
(1752)
Family
:
Eukaryotic proteases
(1343)
Protein domain
:
Factor D
(12)
Human (Homo sapiens) [TaxId: 9606]
(12)
1a
d1fdpa_
A:
1b
d1fdpb_
B:
1c
d1fdpc_
C:
1d
d1fdpd_
D:
[
close SCOP info
]
CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_1fdpA02 (A:28-122,A:233-242)
1b: CATH_1fdpB02 (B:28-122,B:233-240)
1c: CATH_1fdpC02 (C:28-122,C:233-240)
1d: CATH_1fdpD02 (D:28-122,D:233-240)
1e: CATH_1fdpA01 (A:17-27,A:123-232)
1f: CATH_1fdpB01 (B:22-27,B:123-232)
1g: CATH_1fdpD01 (D:22-27,D:123-232)
1h: CATH_1fdpC01 (C:22-27,C:123-232)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Beta Barrel
(4804)
Topology
:
Thrombin, subunit H
(1535)
Homologous Superfamily
:
Trypsin-like serine proteases
(1488)
Human (Homo sapiens)
(615)
1a
1fdpA02
A:28-122,A:233-242
1b
1fdpB02
B:28-122,B:233-240
1c
1fdpC02
C:28-122,C:233-240
1d
1fdpD02
D:28-122,D:233-240
1e
1fdpA01
A:17-27,A:123-232
1f
1fdpB01
B:22-27,B:123-232
1g
1fdpD01
D:22-27,D:123-232
1h
1fdpC01
C:22-27,C:123-232
[
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
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 (143 KB)
Header - Asym.Unit
Biol.Unit 1 (40 KB)
Header - Biol.Unit 1
Biol.Unit 2 (37 KB)
Header - Biol.Unit 2
Biol.Unit 3 (36 KB)
Header - Biol.Unit 3
Biol.Unit 4 (37 KB)
Header - Biol.Unit 4
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
1FDP
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
