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1OJY
Biol. Unit 2
Info
Asym.Unit (172 KB)
Biol.Unit 1 (85 KB)
Biol.Unit 2 (85 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. Radclif R. A. Dwek, D. J. Evans, B. P. Morgan, R. A. G. Smith, S. M. Lea
Date
:
16 Jul 03 (Deposition) - 07 Jan 04 (Release) - 21 Sep 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,C (1x)
Biol. Unit 2: B,D (1x)
Keywords
:
Regulator Of Complement Pathway, Regulator Of Complement, Decay Acceleration Of C3/C5 Convertases, Pathogen Receptor, Short Consensus Repeat Domains, Plasma, Glycoprotein, Membrane, Gpi-Anchor
(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
(3, 7)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
1c: ACETATE ION (ACTc)
1d: ACETATE ION (ACTd)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
2
Ligand/Ion
ACETATE ION
2
GOL
4
Ligand/Ion
GLYCEROL
3
SO4
1
Ligand/Ion
SULFATE ION
[
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Sites
(7, 7)
Info
All Sites
1: AC2 (SOFTWARE)
2: AC6 (SOFTWARE)
3: AC7 (SOFTWARE)
4: AC8 (SOFTWARE)
5: BC2 (SOFTWARE)
6: BC3 (SOFTWARE)
7: BC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC2
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
2
AC6
SOFTWARE
TYR B:213 , ARG B:214 , TYR D:213 , ARG D:214 , THR D:236 , VAL D:237 , ASN D:238
BINDING SITE FOR RESIDUE SO4 D1255
3
AC7
SOFTWARE
PRO D:134 , ILE D:154 , PHE D:156 , SER D:170 , TRP D:181 , ASP D:183 , PRO D:184 , LEU D:185
BINDING SITE FOR RESIDUE ACT D1256
4
AC8
SOFTWARE
ARG B:214 , GLN B:215 , SER B:216 , GLN D:141 , ASN D:159 , THR D:160 , HOH D:2024
BINDING SITE FOR RESIDUE GOL B1256
5
BC2
SOFTWARE
PHE D:156 , SER D:157 , CYS D:158 , LYS D:163 , LEU D:164 , ASP D:240
BINDING SITE FOR RESIDUE GOL D1257
6
BC3
SOFTWARE
PRO D:7 , ASP D:9 , VAL D:10 , ALA D:13 , GLN D:14 , PRO D:15
BINDING SITE FOR RESIDUE GOL D1258
7
BC4
SOFTWARE
ARG A:252 , ARG B:138 , GLN D:215 , SER D:216
BINDING SITE FOR RESIDUE GOL D1259
[
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SAPs(SNPs)/Variants
(6, 12)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_001997 (R20L, chain B/D, )
2: VAR_001998 (R20P, chain B/D, )
3: VAR_001999 (L50R, chain B/D, )
4: VAR_002000 (S167L, chain B/D, )
5: VAR_002001 (A195P, chain B/D, )
6: VAR_015884 (R208H, chain B/D, )
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
B/D
R
20
L
2
UniProt
VAR_001998
R
52
P
DAF_HUMAN
Polymorphism
28371588
B/D
R
20
P
3
UniProt
VAR_001999
L
82
R
DAF_HUMAN
Polymorphism
147474393
B/D
L
50
R
4
UniProt
VAR_002000
S
199
L
DAF_HUMAN
Polymorphism
56283594
B/D
S
167
L
5
UniProt
VAR_002001
A
227
P
DAF_HUMAN
Polymorphism
60822373
B/D
A
195
P
6
UniProt
VAR_015884
R
240
H
DAF_HUMAN
Polymorphism
---
B/D
R
208
H
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(1, 8)
Info
All PROSITE Patterns/Profiles
1: SUSHI (B:64-128,B:3-62,B:129-190,B:191-25...)
;
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
-
B:64-128
-
D:64-128
-
B:3-62
-
D:3-62
-
B:129-190
-
D:129-190
-
B:191-253
-
D:191-253
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]
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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 16)
Info
All SCOP Domains
1a: SCOP_d1ojya1 (A:2-64)
1b: SCOP_d1ojya2 (A:65-128)
1c: SCOP_d1ojya3 (A:129-190)
1d: SCOP_d1ojya4 (A:191-253)
1e: SCOP_d1ojyb1 (B:2-64)
1f: SCOP_d1ojyb2 (B:65-128)
1g: SCOP_d1ojyb3 (B:129-190)
1h: SCOP_d1ojyb4 (B:191-254)
1i: SCOP_d1ojyc1 (C:1-64)
1j: SCOP_d1ojyc2 (C:65-128)
1k: SCOP_d1ojyc3 (C:129-190)
1l: SCOP_d1ojyc4 (C:191-253)
1m: SCOP_d1ojyd1 (D:2-64)
1n: SCOP_d1ojyd2 (D:65-128)
1o: SCOP_d1ojyd3 (D:129-190)
1p: SCOP_d1ojyd4 (D:191-254)
View:
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(
)
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)
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)
(
)
Superfamilies
(
)
(
)
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
d1ojya1
A:2-64
1b
d1ojya2
A:65-128
1c
d1ojya3
A:129-190
1d
d1ojya4
A:191-253
1e
d1ojyb1
B:2-64
1f
d1ojyb2
B:65-128
1g
d1ojyb3
B:129-190
1h
d1ojyb4
B:191-254
1i
d1ojyc1
C:1-64
1j
d1ojyc2
C:65-128
1k
d1ojyc3
C:129-190
1l
d1ojyc4
C:191-253
1m
d1ojyd1
D:2-64
1n
d1ojyd2
D:65-128
1o
d1ojyd3
D:129-190
1p
d1ojyd4
D:191-254
[
close SCOP info
]
CATH Domains
(1, 16)
Info
all CATH domains
1a: CATH_1ojyA04 (A:192-253)
1b: CATH_1ojyC04 (C:192-253)
1c: CATH_1ojyB04 (B:192-254)
1d: CATH_1ojyD04 (D:192-254)
1e: CATH_1ojyA03 (A:129-191)
1f: CATH_1ojyB03 (B:129-191)
1g: CATH_1ojyC03 (C:129-191)
1h: CATH_1ojyD03 (D:129-191)
1i: CATH_1ojyA01 (A:2-64)
1j: CATH_1ojyB01 (B:2-64)
1k: CATH_1ojyD01 (D:2-64)
1l: CATH_1ojyC01 (C:1-64)
1m: CATH_1ojyA02 (A:65-128)
1n: CATH_1ojyB02 (B:65-128)
1o: CATH_1ojyC02 (C:65-128)
1p: CATH_1ojyD02 (D:65-128)
View:
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)
(
)
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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
1ojyA04
A:192-253
1b
1ojyC04
C:192-253
1c
1ojyB04
B:192-254
1d
1ojyD04
D:192-254
1e
1ojyA03
A:129-191
1f
1ojyB03
B:129-191
1g
1ojyC03
C:129-191
1h
1ojyD03
D:129-191
1i
1ojyA01
A:2-64
1j
1ojyB01
B:2-64
1k
1ojyD01
D:2-64
1l
1ojyC01
C:1-64
1m
1ojyA02
A:65-128
1n
1ojyB02
B:65-128
1o
1ojyC02
C:65-128
1p
1ojyD02
D:65-128
[
close CATH info
]
Pfam Domains
(1, 16)
Info
all PFAM domains
1a: PFAM_Sushi_1ojyD01 (D:193-251)
1b: PFAM_Sushi_1ojyD02 (D:193-251)
1c: PFAM_Sushi_1ojyD03 (D:193-251)
1d: PFAM_Sushi_1ojyD04 (D:193-251)
1e: PFAM_Sushi_1ojyD05 (D:193-251)
1f: PFAM_Sushi_1ojyD06 (D:193-251)
1g: PFAM_Sushi_1ojyD07 (D:193-251)
1h: PFAM_Sushi_1ojyD08 (D:193-251)
1i: PFAM_Sushi_1ojyD09 (D:193-251)
1j: PFAM_Sushi_1ojyD10 (D:193-251)
1k: PFAM_Sushi_1ojyD11 (D:193-251)
1l: PFAM_Sushi_1ojyD12 (D:193-251)
1m: PFAM_Sushi_1ojyD13 (D:193-251)
1n: PFAM_Sushi_1ojyD14 (D:193-251)
1o: PFAM_Sushi_1ojyD15 (D:193-251)
1p: PFAM_Sushi_1ojyD16 (D:193-251)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: Sushi]
(50)
Family
:
Sushi
(50)
Homo sapiens (Human)
(42)
1a
Sushi-1ojyD01
D:193-251
1b
Sushi-1ojyD02
D:193-251
1c
Sushi-1ojyD03
D:193-251
1d
Sushi-1ojyD04
D:193-251
1e
Sushi-1ojyD05
D:193-251
1f
Sushi-1ojyD06
D:193-251
1g
Sushi-1ojyD07
D:193-251
1h
Sushi-1ojyD08
D:193-251
1i
Sushi-1ojyD09
D:193-251
1j
Sushi-1ojyD10
D:193-251
1k
Sushi-1ojyD11
D:193-251
1l
Sushi-1ojyD12
D:193-251
1m
Sushi-1ojyD13
D:193-251
1n
Sushi-1ojyD14
D:193-251
1o
Sushi-1ojyD15
D:193-251
1p
Sushi-1ojyD16
D:193-251
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Asymmetric Unit 1
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