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1OK9
Asym. Unit
Info
Asym.Unit (89 KB)
Biol.Unit 1 (84 KB)
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(1)
Title
:
DECAY ACCELERATING FACTOR (CD55): THE STRUCTURE OF AN INTACT HUMAN COMPLEMENT REGULATOR.
Authors
:
P. Lukacik, P. Roversi, J. White, D. Esser, G. P. Smith, J. Billington, P. A. Williams, P. M. Rudd, M. R. Wormald, M. D. M. Crispin, C. M. Radcliffe, R. A. Dwek, D. J. Evans, B. P. Morgan, R. A. G. Smith, S. M. Lea
Date
:
21 Jul 03 (Deposition) - 07 Jan 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Regulator Of Complement Pathway, Regulator Of Complement, Decay Acceleration Of C3/C5 Convertases, Pathogen Receptor, Short Consensus Repeat Domains, Immune System Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. Lukacik, P. Roversi, J. White, D. Esser, G. P. Smith, J. Billington, P. A. Williams, P. M. Rudd, M. R. Wormald, D. J. Harvey, M. D. M. Crispin, C. M. Radcliffe, R. A. Dwek, D. J. Evans, B. P. Morgan, R. A. G. Smith, S. M. Lea
Complement Regulation At The Molecular Level: The Structure Of Decay-Accelerating Factor
Proc. Natl. Acad. Sci. Usa V. 101 1279 2004
(for further references see the
PDB file header
)
[
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Hetero Components
(5, 14)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
1c: ACETATE ION (ACTc)
1d: ACETATE ION (ACTd)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
4a: PLATINUM (II) ION (PTa)
4b: PLATINUM (II) ION (PTb)
5a: SULFATE ION (SO4a)
5b: SULFATE ION (SO4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
4
Ligand/Ion
ACETATE ION
2
CL
4
Ligand/Ion
CHLORIDE ION
3
GOL
2
Ligand/Ion
GLYCEROL
4
PT
2
Ligand/Ion
PLATINUM (II) ION
5
SO4
2
Ligand/Ion
SULFATE ION
[
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Sites
(14, 14)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PRO A:134 , ILE A:154 , PHE A:156 , SER A:170 , TRP A:181 , ASP A:183 , PRO A:184 , LEU A:185
BINDING SITE FOR RESIDUE ACT A1255
02
AC2
SOFTWARE
ARG A:208 , ASP A:209 , HIS A:210
BINDING SITE FOR RESIDUE ACT A1256
03
AC3
SOFTWARE
TYR A:219 , MET A:227 , HIS A:231 , CL A:1258 , CL A:1259
BINDING SITE FOR RESIDUE PT A1257
04
AC4
SOFTWARE
HIS A:231 , PT A:1257 , CL A:1259 , ASN B:133 , PRO B:134
BINDING SITE FOR RESIDUE CL A1258
05
AC5
SOFTWARE
MET A:227 , HIS A:231 , PT A:1257 , CL A:1258 , VAL B:144
BINDING SITE FOR RESIDUE CL A1259
06
AC6
SOFTWARE
TYR A:213 , ARG A:214 , THR A:236 , VAL A:237 , TYR B:213 , ARG B:214
BINDING SITE FOR RESIDUE SO4 A1260
07
AC7
SOFTWARE
PRO B:134 , ILE B:154 , PHE B:156 , SER B:170 , TRP B:181 , ASP B:183 , PRO B:184 , LEU B:185
BINDING SITE FOR RESIDUE ACT B1255
08
AC8
SOFTWARE
LEU B:72 , ASN B:73 , SER B:74
BINDING SITE FOR RESIDUE ACT B1256
09
AC9
SOFTWARE
MET B:227 , HIS B:231 , CL B:1258 , CL B:1259
BINDING SITE FOR RESIDUE PT B1257
10
BC1
SOFTWARE
MET B:227 , GLY B:229 , PT B:1257 , CL B:1259
BINDING SITE FOR RESIDUE CL B1258
11
BC2
SOFTWARE
HIS B:231 , PT B:1257 , CL B:1258
BINDING SITE FOR RESIDUE CL B1259
12
BC3
SOFTWARE
SER B:36 , PHE B:37 , VAL B:38 , SER B:65 , GLU B:67
BINDING SITE FOR RESIDUE SO4 B1260
13
BC4
SOFTWARE
GLU B:136 , ARG B:138
BINDING SITE FOR RESIDUE GOL B1261
14
BC5
SOFTWARE
ASP B:9 , PRO B:11 , ILE B:58
BINDING SITE FOR RESIDUE GOL B1262
[
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]
SAPs(SNPs)/Variants
(6, 12)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_001997 (R20L, chain A/B, )
2: VAR_001998 (R20P, chain A/B, )
3: VAR_001999 (L50R, chain A/B, )
4: VAR_002000 (S167L, chain A/B, )
5: VAR_002001 (A195P, chain A/B, )
6: VAR_015884 (R208H, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_001997
R
52
L
DAF_HUMAN
Polymorphism
28371588
A/B
R
20
L
2
UniProt
VAR_001998
R
52
P
DAF_HUMAN
Polymorphism
28371588
A/B
R
20
P
3
UniProt
VAR_001999
L
82
R
DAF_HUMAN
Polymorphism
147474393
A/B
L
50
R
4
UniProt
VAR_002000
S
199
L
DAF_HUMAN
Polymorphism
56283594
A/B
S
167
L
5
UniProt
VAR_002001
A
227
P
DAF_HUMAN
Polymorphism
60822373
A/B
A
195
P
6
UniProt
VAR_015884
R
240
H
DAF_HUMAN
Polymorphism
---
A/B
R
208
H
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 8)
Info
All PROSITE Patterns/Profiles
1: SUSHI (A:64-128,B:64-128|A:3-62,B:3-62|A:...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
SUSHI
PS50923
Sushi/CCP/SCR domain profile.
DAF_HUMAN
96-160
34-94
161-222
223-285
8
A:64-128
B:64-128
A:3-62
B:3-62
A:129-190
B:129-190
A:191-253
B:191-253
[
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]
Exons
(7, 14)
Info
All Exons
Exon 1.1a (A:1-2 | B:1-2)
Exon 1.3 (A:2-64 | B:2-64)
Exon 1.4b (A:64-128 | B:64-128)
Exon 1.5 (A:128-161 | B:128-161)
Exon 1.6 (A:161-190 | B:161-190)
Exon 1.7 (A:190-253 | B:190-253)
Exon 1.8b (A:253-254 | B:253-254)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.1a
2: Boundary 1.1a/1.3
3: Boundary 1.3/1.4b
4: Boundary 1.4b/1.5
5: Boundary 1.5/1.6
6: Boundary 1.6/1.7
7: Boundary 1.7/1.8b
8: Boundary 1.8b/1.8d
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
1.1a
ENST00000367064
1a
ENSE00001840627
chr1:
207494853-207495210
358
DAF_HUMAN
1-34
34
2
A:1-2
B:1-2
2
2
1.3
ENST00000367064
3
ENSE00001443405
chr1:
207495727-207495912
186
DAF_HUMAN
34-96
63
2
A:2-64
B:2-64
63
63
1.4b
ENST00000367064
4b
ENSE00001443404
chr1:
207497904-207498095
192
DAF_HUMAN
96-160
65
2
A:64-128
B:64-128
65
65
1.5
ENST00000367064
5
ENSE00001069638
chr1:
207498967-207499066
100
DAF_HUMAN
160-193
34
2
A:128-161
B:128-161
34
34
1.6
ENST00000367064
6
ENSE00001069637
chr1:
207500097-207500182
86
DAF_HUMAN
193-222
30
2
A:161-190
B:161-190
30
30
1.7
ENST00000367064
7
ENSE00000960173
chr1:
207504453-207504641
189
DAF_HUMAN
222-285
64
2
A:190-253
B:190-253
64
64
1.8b
ENST00000367064
8b
ENSE00001041396
chr1:
207510038-207510163
126
DAF_HUMAN
285-327
43
2
A:253-254
B:253-254
2
2
1.8d
ENST00000367064
8d
ENSE00001253047
chr1:
207510674-207510754
81
DAF_HUMAN
327-354
28
0
-
-
1.9
ENST00000367064
9
ENSE00001432766
chr1:
207512742-207512762
21
DAF_HUMAN
354-361
8
0
-
-
1.15f
ENST00000367064
15f
ENSE00001631743
chr1:
207532891-207534311
1421
DAF_HUMAN
361-381
21
0
-
-
[
close EXON info
]
SCOP Domains
(1, 8)
Info
All SCOP Domains
1a: SCOP_d1ok9a1 (A:1-64)
1b: SCOP_d1ok9a2 (A:65-128)
1c: SCOP_d1ok9a3 (A:129-190)
1d: SCOP_d1ok9a4 (A:191-254)
1e: SCOP_d1ok9b1 (B:1-64)
1f: SCOP_d1ok9b2 (B:65-128)
1g: SCOP_d1ok9b3 (B:129-190)
1h: SCOP_d1ok9b4 (B:191-254)
View:
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Classes
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)
(
)
Folds
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)
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)
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(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Small proteins
(3458)
Fold
:
Complement control module/SCR domain
(70)
Superfamily
:
Complement control module/SCR domain
(70)
Family
:
Complement control module/SCR domain
(67)
Protein domain
:
Complement decay-accelerating factor (Daf, CD55)
(18)
Human (Homo sapiens) [TaxId: 9606]
(18)
1a
d1ok9a1
A:1-64
1b
d1ok9a2
A:65-128
1c
d1ok9a3
A:129-190
1d
d1ok9a4
A:191-254
1e
d1ok9b1
B:1-64
1f
d1ok9b2
B:65-128
1g
d1ok9b3
B:129-190
1h
d1ok9b4
B:191-254
[
close SCOP info
]
CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_1ok9A04 (A:192-254)
1b: CATH_1ok9B04 (B:192-254)
1c: CATH_1ok9A03 (A:129-191)
1d: CATH_1ok9B03 (B:129-191)
1e: CATH_1ok9A01 (A:1-64)
1f: CATH_1ok9B01 (B:1-64)
1g: CATH_1ok9A02 (A:65-128)
1h: CATH_1ok9B02 (B:65-128)
View:
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Classes
(
)
(
)
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(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Ribbon
(789)
Topology
:
Complement Module; domain 1
(62)
Homologous Superfamily
:
Complement Module, domain 1
(60)
Human (Homo sapiens)
(46)
1a
1ok9A04
A:192-254
1b
1ok9B04
B:192-254
1c
1ok9A03
A:129-191
1d
1ok9B03
B:129-191
1e
1ok9A01
A:1-64
1f
1ok9B01
B:1-64
1g
1ok9A02
A:65-128
1h
1ok9B02
B:65-128
[
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]
Pfam Domains
(1, 8)
Info
all PFAM domains
1a: PFAM_Sushi_1ok9B01 (B:193-251)
1b: PFAM_Sushi_1ok9B02 (B:193-251)
1c: PFAM_Sushi_1ok9B03 (B:193-251)
1d: PFAM_Sushi_1ok9B04 (B:193-251)
1e: PFAM_Sushi_1ok9B05 (B:193-251)
1f: PFAM_Sushi_1ok9B06 (B:193-251)
1g: PFAM_Sushi_1ok9B07 (B:193-251)
1h: PFAM_Sushi_1ok9B08 (B:193-251)
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Clans
(
)
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)
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(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: Sushi]
(50)
Family
:
Sushi
(50)
Homo sapiens (Human)
(42)
1a
Sushi-1ok9B01
B:193-251
1b
Sushi-1ok9B02
B:193-251
1c
Sushi-1ok9B03
B:193-251
1d
Sushi-1ok9B04
B:193-251
1e
Sushi-1ok9B05
B:193-251
1f
Sushi-1ok9B06
B:193-251
1g
Sushi-1ok9B07
B:193-251
1h
Sushi-1ok9B08
B:193-251
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