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2XWB
Biol. Unit 4
Info
Asym.Unit (1.7 MB)
Biol.Unit 1 (856 KB)
Biol.Unit 2 (860 KB)
Biol.Unit 3 (859 KB)
Biol.Unit 4 (856 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF COMPLEMENT C3B IN COMPLEX WITH FACTORS B AND D
Authors
:
F. Forneris, D. Ricklin, J. Wu, A. Tzekou, R. S. Wallace, J. D. Lambris, P
Date
:
01 Nov 10 (Deposition) - 12 Jan 11 (Release) - 11 Apr 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.49
Chains
:
Asym. Unit : A,B,C,D,F,H,I,J
Biol. Unit 1: A,B,F,J (1x)
Biol. Unit 2: C,D,H,I (1x)
Biol. Unit 3: C,D,H,J (1x)
Biol. Unit 4: A,B,F,I (1x)
Keywords
:
Immune System, Pro-Convertase, Hydrolase, Serine Protease, Conformational Changes, Alternative Pathway
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
F. Forneris, D. Ricklin, J. Wu, A. Tzekou, R. S. Wallace, J. D. Lambris, P. Gros
Structures Of C3B In Complex With Factors B And D Give Insight Into Complement Convertase Formation.
Science V. 330 1816 2010
[
close entry info
]
Hetero Components
(3, 10)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
1b: BETA-D-MANNOSE (BMAb)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
4a: N-ACETYL-D-GLUCOSAMINE (NAGa)
4b: N-ACETYL-D-GLUCOSAMINE (NAGb)
4c: N-ACETYL-D-GLUCOSAMINE (NAGc)
4d: N-ACETYL-D-GLUCOSAMINE (NAGd)
4e: N-ACETYL-D-GLUCOSAMINE (NAGe)
4f: N-ACETYL-D-GLUCOSAMINE (NAGf)
4g: N-ACETYL-D-GLUCOSAMINE (NAGg)
4h: N-ACETYL-D-GLUCOSAMINE (NAGh)
4i: N-ACETYL-D-GLUCOSAMINE (NAGi)
4j: N-ACETYL-D-GLUCOSAMINE (NAGj)
4k: N-ACETYL-D-GLUCOSAMINE (NAGk)
4l: N-ACETYL-D-GLUCOSAMINE (NAGl)
4m: N-ACETYL-D-GLUCOSAMINE (NAGm)
4n: N-ACETYL-D-GLUCOSAMINE (NAGn)
4o: N-ACETYL-D-GLUCOSAMINE (NAGo)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
1
Ligand/Ion
BETA-D-MANNOSE
2
GOL
1
Ligand/Ion
GLYCEROL
3
MG
-1
Ligand/Ion
MAGNESIUM ION
4
NAG
8
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC4 (SOFTWARE)
3: AC5 (SOFTWARE)
4: AC6 (SOFTWARE)
5: BC1 (SOFTWARE)
6: BC3 (SOFTWARE)
7: BC4 (SOFTWARE)
8: BC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
PRO A:505 , ASP A:532 , VAL A:533 , ASP A:535
BINDING SITE FOR RESIDUE MG A1645
2
AC4
SOFTWARE
ASN B:1641 , SER F:253 , SER F:255 , THR F:328 , HOH F:2001 , HOH F:2002
BINDING SITE FOR RESIDUE MG F1742
3
AC5
SOFTWARE
TYR F:95 , ASN F:97
BINDING SITE FOR RESIDUE NAG F1743
4
AC6
SOFTWARE
ASN F:353 , ASN F:392
BINDING SITE FOR RESIDUE NAG F1747
5
BC1
SOFTWARE
ASP I:116 , VAL I:117 , VAL I:148 , LEU I:149 , ARG I:151 , MET I:169 , CYS I:170
BINDING SITE FOR RESIDUE GOL I1229
6
BC3
SOFTWARE
ASN A:63 , ALA A:481
BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 63 RESIDUES 1643 TO 1644
7
BC4
SOFTWARE
MET B:916 , ASN B:917
BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 917 RESIDUES 2642 TO 2643
8
BC6
SOFTWARE
ASN F:117
BINDING SITE FOR CHAIN F OF SUGAR BOUND TO ASN F 117 RESIDUES 1117 TO 1119
[
close Site info
]
SAPs(SNPs)/Variants
(36, 36)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_001983 (R80G, chain A, )
02: VAR_070941 (K133Q, chain A, )
03: VAR_063659 (S141P, chain F, )
04: VAR_063660 (R178Q, chain F, )
05: VAR_034866 (V188G, chain I, )
06: VAR_034867 (C189R, chain I, )
07: VAR_063661 (I217L, chain F, )
08: VAR_034868 (I223M, chain I, )
09: VAR_063221 (F261L, chain F, )
10: VAR_001984 (P292L, chain A, )
11: VAR_063222 (K298E, chain F, )
12: VAR_063662 (K298Q, chain F, )
13: VAR_063663 (M433I, chain F, )
14: VAR_020262 (E447D, chain A, )
15: VAR_063664 (K508R, chain F, )
16: VAR_001985 (D527N, chain A, )
17: VAR_016277 (K540E, chain F, )
18: VAR_063213 (R570Q, chain A, )
19: VAR_063214 (R570W, chain A, )
20: VAR_063654 (F581V, chain A, )
21: VAR_016278 (D626E, chain F, )
22: VAR_006495 (A711S, chain F, )
23: VAR_019206 (R841K, chain B, )
24: VAR_063655 (R1020L, chain B, )
25: VAR_063216 (A1072V, chain B, )
26: VAR_063217 (D1093N, chain B, )
27: VAR_063218 (C1136W, chain B, )
28: VAR_063219 (Q1139K, chain B, )
29: VAR_022761 (D1194N, chain B, )
30: VAR_019207 (G1202D, chain B, )
31: VAR_001986 (R1298Q, chain B, )
32: VAR_019208 (I1345T, chain B, )
33: VAR_063220 (H1442D, chain B, )
34: VAR_029792 (Q1499R, chain B, )
35: VAR_029793 (H1579N, chain B, )
36: VAR_029326 (S1597R, chain B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_001983
R
102
G
CO3_HUMAN
Polymorphism
2230199
A
R
80
G
02
UniProt
VAR_070941
K
155
Q
CO3_HUMAN
Disease (ARMD9)
---
A
K
133
Q
03
UniProt
VAR_063659
S
166
P
CFAB_HUMAN
Disease (AHUS4)
---
F
S
141
P
04
UniProt
VAR_063660
R
203
Q
CFAB_HUMAN
Disease (AHUS4)
---
F
R
178
Q
05
UniProt
VAR_034866
V
213
G
CFAD_HUMAN
Disease (CFDD)
---
I
V
188
G
06
UniProt
VAR_034867
C
214
R
CFAD_HUMAN
Disease (CFDD)
---
I
C
189
R
07
UniProt
VAR_063661
I
242
L
CFAB_HUMAN
Disease (AHUS4)
---
F
I
217
L
08
UniProt
VAR_034868
I
248
M
CFAD_HUMAN
Polymorphism
2230216
I
I
223
M
09
UniProt
VAR_063221
F
286
L
CFAB_HUMAN
Disease (AHUS4)
---
F
F
261
L
10
UniProt
VAR_001984
P
314
L
CO3_HUMAN
Polymorphism
1047286
A
P
292
L
11
UniProt
VAR_063222
K
323
E
CFAB_HUMAN
Disease (AHUS4)
---
F
K
298
E
12
UniProt
VAR_063662
K
323
Q
CFAB_HUMAN
Disease (AHUS4)
---
F
K
298
Q
13
UniProt
VAR_063663
M
458
I
CFAB_HUMAN
Disease (AHUS4)
---
F
M
433
I
14
UniProt
VAR_020262
E
469
D
CO3_HUMAN
Polymorphism
11569422
A
E
447
D
15
UniProt
VAR_063664
K
533
R
CFAB_HUMAN
Disease (AHUS4)
---
F
K
508
R
16
UniProt
VAR_001985
D
549
N
CO3_HUMAN
Disease (C3D)
---
A
D
527
N
17
UniProt
VAR_016277
K
565
E
CFAB_HUMAN
Polymorphism
4151659
F
K
540
E
18
UniProt
VAR_063213
R
592
Q
CO3_HUMAN
Disease (AHUS5)
---
A
R
570
Q
19
UniProt
VAR_063214
R
592
W
CO3_HUMAN
Disease (AHUS5)
---
A
R
570
W
20
UniProt
VAR_063654
F
603
V
CO3_HUMAN
Disease (AHUS5)
---
A
F
581
V
21
UniProt
VAR_016278
D
651
E
CFAB_HUMAN
Polymorphism
4151660
F
D
626
E
22
UniProt
VAR_006495
A
736
S
CFAB_HUMAN
Polymorphism
---
F
A
711
S
23
UniProt
VAR_019206
R
863
K
CO3_HUMAN
Polymorphism
11569472
B
R
841
K
24
UniProt
VAR_063655
R
1042
L
CO3_HUMAN
Disease (AHUS5)
---
B
R
1020
L
25
UniProt
VAR_063216
A
1094
V
CO3_HUMAN
Disease (AHUS5)
---
B
A
1072
V
26
UniProt
VAR_063217
D
1115
N
CO3_HUMAN
Disease (AHUS5)
---
B
D
1093
N
27
UniProt
VAR_063218
C
1158
W
CO3_HUMAN
Disease (AHUS5)
---
B
C
1136
W
28
UniProt
VAR_063219
Q
1161
K
CO3_HUMAN
Disease (AHUS5)
---
B
Q
1139
K
29
UniProt
VAR_022761
D
1216
N
CO3_HUMAN
Unclassified
---
B
D
1194
N
30
UniProt
VAR_019207
G
1224
D
CO3_HUMAN
Polymorphism
11569534
B
G
1202
D
31
UniProt
VAR_001986
R
1320
Q
CO3_HUMAN
Disease (C3D)
---
B
R
1298
Q
32
UniProt
VAR_019208
I
1367
T
CO3_HUMAN
Polymorphism
11569541
B
I
1345
T
33
UniProt
VAR_063220
H
1464
D
CO3_HUMAN
Disease (AHUS5)
---
B
H
1442
D
34
UniProt
VAR_029792
Q
1521
R
CO3_HUMAN
Polymorphism
7256789
B
Q
1499
R
35
UniProt
VAR_029793
H
1601
N
CO3_HUMAN
Polymorphism
1803225
B
H
1579
N
36
UniProt
VAR_029326
S
1619
R
CO3_HUMAN
Polymorphism
2230210
B
S
1597
R
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(7, 12)
Info
All PROSITE Patterns/Profiles
1: TRYPSIN_DOM (I:1-228)
2: SUSHI (F:10-75)
3: TRYPSIN_HIS (I:37-42)
4: TRYPSIN_SER (I:177-188)
5: VWFA (F:245-444)
6: ALPHA_2_MACROGLOBULIN (B:985-993)
7: NTR (B:1496-1639)
;
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
I:1-228
-
CFAB_HUMAN
477-757
1
F:452-732
-
2
SUSHI
PS50923
Sushi/CCP/SCR domain profile.
CFAB_HUMAN
35-100
101-160
163-220
3
F:10-75
-
F:76-135
-
F:138-195
-
3
TRYPSIN_HIS
PS00134
Serine proteases, trypsin family, histidine active site.
CFAD_HUMAN
62-67
1
I:37-42
-
CFAB_HUMAN
522-527
1
F:497-502
-
4
TRYPSIN_SER
PS00135
Serine proteases, trypsin family, serine active site.
CFAD_HUMAN
202-213
1
I:177-188
-
CFAB_HUMAN
693-704
1
F:668-679
-
5
VWFA
PS50234
VWFA domain profile.
CFAB_HUMAN
270-469
1
F:245-444
-
6
ALPHA_2_MACROGLOBULIN
PS00477
Alpha-2-macroglobulin family thiolester region signature.
CO3_HUMAN
1007-1015
1
B:985-993
-
7
NTR
PS50189
NTR domain profile.
CO3_HUMAN
1518-1661
1
B:1496-1639
-
[
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.
(no "Exon" information available for biological units yet)
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
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]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(10, 26)
Info
all PFAM domains
01a: PFAM_A2M_comp_2xwbD01 (D:1029-1262)
01b: PFAM_A2M_comp_2xwbD02 (D:1029-1262)
02a: PFAM_A2M_N_2xwbC01 (C:107-202)
02b: PFAM_A2M_N_2xwbC02 (C:107-202)
03a: PFAM_A2M_2xwbD03 (D:748-844)
03b: PFAM_A2M_2xwbD04 (D:748-844)
04a: PFAM_Trypsin_2xwbH01 (H:456-727)
04b: PFAM_Trypsin_2xwbH02 (H:456-727)
04c: PFAM_Trypsin_2xwbJ01 (J:1-223)
04d: PFAM_Trypsin_2xwbJ02 (J:1-223)
05a: PFAM_NTR_2xwbD05 (D:1512-1622)
05b: PFAM_NTR_2xwbD06 (D:1512-1622)
06a: PFAM_A2M_N_2_2xwbC03 (C:434-583)
06b: PFAM_A2M_N_2_2xwbC04 (C:434-583)
07a: PFAM_A2M_recep_2xwbD07 (D:1376-1471)
07b: PFAM_A2M_recep_2xwbD08 (D:1376-1471)
08a: PFAM_Sushi_2xwbH03 (H:140-193)
08b: PFAM_Sushi_2xwbH04 (H:140-193)
08c: PFAM_Sushi_2xwbH05 (H:140-193)
08d: PFAM_Sushi_2xwbH06 (H:140-193)
08e: PFAM_Sushi_2xwbH07 (H:140-193)
08f: PFAM_Sushi_2xwbH08 (H:140-193)
09a: PFAM_Thiol_ester_cl_2xwbD09 (D:977-1007)
09b: PFAM_Thiol_ester_cl_2xwbD10 (D:977-1007)
10a: PFAM_VWA_2xwbH09 (H:245-443)
10b: PFAM_VWA_2xwbH10 (H:245-443)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
6_Hairpin
(120)
Family
:
A2M_comp
(16)
Homo sapiens (Human)
(13)
01a
A2M_comp-2xwbD01
D:1029-1262
01b
A2M_comp-2xwbD02
D:1029-1262
Clan
:
E-set
(290)
Family
:
A2M_N
(14)
Homo sapiens (Human)
(13)
02a
A2M_N-2xwbC01
C:107-202
02b
A2M_N-2xwbC02
C:107-202
Clan
:
Ig
(577)
Family
:
A2M
(13)
Homo sapiens (Human)
(12)
03a
A2M-2xwbD03
D:748-844
03b
A2M-2xwbD04
D:748-844
Clan
:
Peptidase_PA
(797)
Family
:
Trypsin
(679)
Homo sapiens (Human)
(339)
04a
Trypsin-2xwbH01
H:456-727
04b
Trypsin-2xwbH02
H:456-727
04c
Trypsin-2xwbJ01
J:1-223
04d
Trypsin-2xwbJ02
J:1-223
Clan
:
TIMP-like
(15)
Family
:
NTR
(13)
Homo sapiens (Human)
(13)
05a
NTR-2xwbD05
D:1512-1622
05b
NTR-2xwbD06
D:1512-1622
Clan
:
no clan defined [family: A2M_N_2]
(13)
Family
:
A2M_N_2
(13)
Homo sapiens (Human)
(12)
06a
A2M_N_2-2xwbC03
C:434-583
06b
A2M_N_2-2xwbC04
C:434-583
Clan
:
no clan defined [family: A2M_recep]
(13)
Family
:
A2M_recep
(13)
Homo sapiens (Human)
(12)
07a
A2M_recep-2xwbD07
D:1376-1471
07b
A2M_recep-2xwbD08
D:1376-1471
Clan
:
no clan defined [family: Sushi]
(50)
Family
:
Sushi
(50)
Homo sapiens (Human)
(42)
08a
Sushi-2xwbH03
H:140-193
08b
Sushi-2xwbH04
H:140-193
08c
Sushi-2xwbH05
H:140-193
08d
Sushi-2xwbH06
H:140-193
08e
Sushi-2xwbH07
H:140-193
08f
Sushi-2xwbH08
H:140-193
Clan
:
no clan defined [family: Thiol-ester_cl]
(12)
Family
:
Thiol-ester_cl
(12)
Homo sapiens (Human)
(9)
09a
Thiol-ester_cl-2xwbD09
D:977-1007
09b
Thiol-ester_cl-2xwbD10
D:977-1007
Clan
:
vWA-like
(60)
Family
:
VWA
(50)
Homo sapiens (Human)
(47)
10a
VWA-2xwbH09
H:245-443
10b
VWA-2xwbH10
H:245-443
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Asym.Unit (1.7 MB)
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