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2J3O
Asym. Unit
Info
Asym.Unit (223 KB)
Biol.Unit 1 (111 KB)
Biol.Unit 2 (109 KB)
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(1)
Title
:
L-FICOLIN COMPLEXED TO N-ACETYL-D-GLUCOSAMINE
Authors
:
V. Garlatti, C. Gaboriaud
Date
:
22 Aug 06 (Deposition) - 23 Jan 07 (Release) - 12 Oct 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.65
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C (1x)
Biol. Unit 2: D,E,F (1x)
Keywords
:
Sugar Binding Protein, Lectin, Collagen, Immunology, Glycoprotein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
V. Garlatti, N. Belloy, L. Martin, M. Lacroix, M. Matsushita, Y. Endo, T. Fujita, J. C. Fontecilla-Camps, G. J. Arlaud, N. M. Thielens, C. Gaboriaud
Structural Insights Into The Innate Immune Recognition Specificities Of L- And H-Ficolins.
Embo J. V. 26 623 2007
[
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Hetero Components
(3, 16)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
2d: CALCIUM ION (CAd)
2e: CALCIUM ION (CAe)
2f: CALCIUM ION (CAf)
3a: N-ACETYL-D-GLUCOSAMINE (NAGa)
3b: N-ACETYL-D-GLUCOSAMINE (NAGb)
3c: N-ACETYL-D-GLUCOSAMINE (NAGc)
3d: N-ACETYL-D-GLUCOSAMINE (NAGd)
3e: N-ACETYL-D-GLUCOSAMINE (NAGe)
3f: N-ACETYL-D-GLUCOSAMINE (NAGf)
3g: N-ACETYL-D-GLUCOSAMINE (NAGg)
3h: N-ACETYL-D-GLUCOSAMINE (NAGh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
2
Ligand/Ion
ACETATE ION
2
CA
6
Ligand/Ion
CALCIUM ION
3
NAG
8
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
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]
Sites
(16, 16)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER A:127 , SER A:143 , LEU A:145 , SER B:91 , CYS B:108 , ASP B:109 , THR B:112 , ARG B:122 , GLU B:282 , LYS B:284 , HOH B:2025
BINDING SITE FOR RESIDUE NAG B1290
02
AC2
SOFTWARE
ASN B:215
BINDING SITE FOR RESIDUE NAG B1293
03
AC3
SOFTWARE
SER A:91 , ASP A:109 , ARG A:122 , GLU A:282 , SER C:127 , VAL C:128 , SER C:143 , LEU C:145
BINDING SITE FOR RESIDUE NAG C1289
04
AC4
SOFTWARE
LEU B:145 , ASP C:109 , ARG C:122 , ASP C:169 , GLU C:282 , LYS C:284 , HOH C:2031
BINDING SITE FOR RESIDUE NAG C1290
05
AC5
SOFTWARE
THR D:112 , ARG D:122 , GLU D:282 , LYS D:284 , HOH D:2019 , HOH D:2020 , SER F:127
BINDING SITE FOR RESIDUE NAG D1288
06
AC6
SOFTWARE
ASP D:125 , SER D:127 , SER D:143 , LEU D:145 , ASP E:109 , ARG E:122 , GLU E:282
BINDING SITE FOR RESIDUE NAG E1289
07
AC7
SOFTWARE
ASP E:125 , SER E:127 , SER E:143 , LEU E:145 , ARG F:122 , GLU F:282
BINDING SITE FOR RESIDUE NAG E1292
08
AC8
SOFTWARE
ASP A:224 , ASP A:226 , ASN A:228 , GLY A:230 , ASN A:231
BINDING SITE FOR RESIDUE CA A1289
09
AC9
SOFTWARE
THR A:105 , ARG A:144 , HIS B:88
BINDING SITE FOR RESIDUE ACT B1289
10
BC1
SOFTWARE
ASP B:224 , ASP B:226 , ASN B:228 , GLY B:230
BINDING SITE FOR RESIDUE CA B1291
11
BC2
SOFTWARE
ASN B:244 , CYS B:245 , HIS B:246 , LEU E:74
BINDING SITE FOR RESIDUE ACT B1292
12
BC3
SOFTWARE
ASP C:224 , ASP C:226 , ASN C:228 , GLY C:230
BINDING SITE FOR RESIDUE CA C1291
13
BC4
SOFTWARE
ASP D:224 , ASP D:226 , ASN D:228 , THR D:229 , GLY D:230
BINDING SITE FOR RESIDUE CA D1289
14
BC5
SOFTWARE
ASP E:224 , ASP E:226 , ASN E:228 , GLY E:230
BINDING SITE FOR RESIDUE CA E1290
15
BC6
SOFTWARE
ASP F:224 , ASP F:226 , ASN F:228 , GLY F:230
BINDING SITE FOR RESIDUE CA F1289
16
BC7
SOFTWARE
ASN E:215
BINDING SITE FOR MONO-SACCHARIDE NAG E1291 BOUND TO ASN E 215
[
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]
SAPs(SNPs)/Variants
(4, 24)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_049072 (H88Y, chain A/B/C/D/E/F, )
2: VAR_049073 (G92S, chain A/B/C/D/E/F, )
3: VAR_049074 (T211M, chain A/B/C/D/E/F, )
4: VAR_049075 (A233S, chain A/B/C/D/E/F, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_049072
H
113
Y
FCN2_HUMAN
Polymorphism
17549179
A/B/C/D/E/F
H
88
Y
2
UniProt
VAR_049073
G
117
S
FCN2_HUMAN
Polymorphism
12684476
A/B/C/D/E/F
G
92
S
3
UniProt
VAR_049074
T
236
M
FCN2_HUMAN
Polymorphism
17549193
A/B/C/D/E/F
T
211
M
4
UniProt
VAR_049075
A
258
S
FCN2_HUMAN
Polymorphism
7851696
A/B/C/D/E/F
A
233
S
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 7)
Info
All PROSITE Patterns/Profiles
1: FIBRINOGEN_C_2 (B:72-288)
2: FIBRINOGEN_C_1 (A:240-252,B:240-252,C:240-252,D:24...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
FIBRINOGEN_C_2
PS51406
Fibrinogen C-terminal domain profile.
FCN2_HUMAN
96-313
1
B:72-288
2
FIBRINOGEN_C_1
PS00514
Fibrinogen C-terminal domain signature.
FCN2_HUMAN
265-277
6
A:240-252
B:240-252
C:240-252
D:240-252
E:240-252
F:240-252
[
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]
Exons
(5, 30)
Info
All Exons
Exon 1.4 (A:72-76 | B:70-76 (gaps) | C:72-76...)
Exon 1.5 (A:76-118 | B:76-118 | C:76-118 | D...)
Exon 1.6 (A:119-162 | B:119-162 | C:119-162 ...)
Exon 1.7 (A:162-207 | B:162-207 | C:162-207 ...)
Exon 1.8a (A:207-288 | B:207-288 | C:207-288 ...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.3a/1.4
2: Boundary 1.4/1.5
3: Boundary 1.5/1.6
4: Boundary 1.6/1.7
5: Boundary 1.7/1.8a
6: Boundary 1.8a/-
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
1.1b
ENST00000291744
1b
ENSE00001890733
chr9:
137772658-137772767
110
FCN2_HUMAN
1-34
34
0
-
-
1.2
ENST00000291744
2
ENSE00001051605
chr9:
137774372-137774485
114
FCN2_HUMAN
34-72
39
0
-
-
1.3a
ENST00000291744
3a
ENSE00001051599
chr9:
137775148-137775201
54
FCN2_HUMAN
72-90
19
0
-
-
1.4
ENST00000291744
4
ENSE00001247525
chr9:
137776586-137776618
33
FCN2_HUMAN
90-101
12
6
A:72-76
B:70-76 (gaps)
C:72-76
D:72-76
E:72-76
F:72-76
5
7
5
5
5
5
1.5
ENST00000291744
5
ENSE00001643405
chr9:
137777085-137777212
128
FCN2_HUMAN
101-143
43
6
A:76-118
B:76-118
C:76-118
D:76-118
E:76-118
F:76-118
43
43
43
43
43
43
1.6
ENST00000291744
6
ENSE00001786911
chr9:
137777614-137777743
130
FCN2_HUMAN
144-187
44
6
A:119-162
B:119-162
C:119-162
D:119-162
E:119-162
F:119-162
44
44
44
44
44
44
1.7
ENST00000291744
7
ENSE00001656900
chr9:
137778276-137778410
135
FCN2_HUMAN
187-232
46
6
A:162-207
B:162-207
C:162-207
D:162-207
E:162-207
F:162-207
46
46
46
46
46
46
1.8a
ENST00000291744
8a
ENSE00001941356
chr9:
137779014-137779366
353
FCN2_HUMAN
232-313
82
6
A:207-288
B:207-288
C:207-288
D:207-287
E:207-288
F:207-288
82
82
82
81
82
82
[
close EXON info
]
SCOP Domains
(1, 6)
Info
All SCOP Domains
1a: SCOP_d2j3oa_ (A:)
1b: SCOP_d2j3ob1 (B:72-288)
1c: SCOP_d2j3oc_ (C:)
1d: SCOP_d2j3od_ (D:)
1e: SCOP_d2j3oe_ (E:)
1f: SCOP_d2j3of_ (F:)
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)
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)
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)
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Fibrinogen C-terminal domain-like
(70)
Superfamily
:
Fibrinogen C-terminal domain-like
(70)
Family
:
automated matches
(27)
Protein domain
:
automated matches
(27)
Human (Homo sapiens) [TaxId: 9606]
(27)
1a
d2j3oa_
A:
1b
d2j3ob1
B:72-288
1c
d2j3oc_
C:
1d
d2j3od_
D:
1e
d2j3oe_
E:
1f
d2j3of_
F:
[
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CATH Domains
(2, 12)
Info
all CATH domains
1a: CATH_2j3oB01 (B:70-206,B:280-288)
1b: CATH_2j3oA01 (A:72-206,A:280-288)
1c: CATH_2j3oC01 (C:72-206,C:280-288)
1d: CATH_2j3oE01 (E:72-206,E:280-288)
1e: CATH_2j3oF01 (F:72-206,F:280-288)
1f: CATH_2j3oD01 (D:72-206,D:280-287)
2a: CATH_2j3oA02 (A:207-279)
2b: CATH_2j3oB02 (B:207-279)
2c: CATH_2j3oC02 (C:207-279)
2d: CATH_2j3oD02 (D:207-279)
2e: CATH_2j3oE02 (E:207-279)
2f: CATH_2j3oF02 (F:207-279)
View:
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(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Gamma Fibrinogen; Chain A, domain 1
(58)
Homologous Superfamily
:
Gamma Fibrinogen, chain A, domain 1
(58)
Human (Homo sapiens)
(53)
1a
2j3oB01
B:70-206,B:280-288
1b
2j3oA01
A:72-206,A:280-288
1c
2j3oC01
C:72-206,C:280-288
1d
2j3oE01
E:72-206,E:280-288
1e
2j3oF01
F:72-206,F:280-288
1f
2j3oD01
D:72-206,D:280-287
Class
:
Few Secondary Structures
(1120)
Architecture
:
Irregular
(1120)
Topology
:
Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2
(58)
Homologous Superfamily
:
Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2
(58)
Human (Homo sapiens)
(53)
2a
2j3oA02
A:207-279
2b
2j3oB02
B:207-279
2c
2j3oC02
C:207-279
2d
2j3oD02
D:207-279
2e
2j3oE02
E:207-279
2f
2j3oF02
F:207-279
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Asym.Unit (223 KB)
Header - Asym.Unit
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Header - Biol.Unit 1
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