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3CA6
Asym. Unit
Info
Asym.Unit (115 KB)
Biol.Unit 1 (108 KB)
Biol.Unit 2 (213 KB)
Biol.Unit 3 (213 KB)
Biol.Unit 4 (213 KB)
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(1)
Title
:
SAMBUCUS NIGRA AGGLUTININ II (SNA-II)- TETRAGONAL CRYSTAL FORM-COMPLEXED TO TN ANTIGEN
Authors
:
L. Maveyraud, L. Mourey
Date
:
19 Feb 08 (Deposition) - 25 Nov 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.40
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Biol. Unit 2: A (2x)
Biol. Unit 3: A (2x)
Biol. Unit 4: A (2x)
Keywords
:
Beta-Trefoil, Ricin-B Domain, Glycosylation, Lectin, Glycoprotein, Sugar Binding Protein, Plant Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. Maveyraud, H. Niwa, V. Guillet, D. I. Svergun, P. V. Konarev, R. A. Palmer, W. J. Peumans, P. Rouge, E. J. Van Damme, C. D. Reynolds, L. Mourey
Structural Basis For Sugar Recognition, Including The Tn Carcinoma Antigen, By The Lectin Sna-Ii From Sambucus Nigra
Proteins V. 75 89 2009
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Hetero Components
(6, 16)
Info
All Hetero Components
1a: N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE (A2Ga)
2a: ACETATE ION (ACTa)
3a: ALPHA-L-FUCOSE (FUCa)
3b: ALPHA-L-FUCOSE (FUCb)
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)
5a: SERINE (SERa)
6a: SULFATE ION (SO4a)
6b: SULFATE ION (SO4b)
6c: SULFATE ION (SO4c)
6d: SULFATE ION (SO4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
A2G
1
Ligand/Ion
N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2
ACT
1
Ligand/Ion
ACETATE ION
3
FUC
2
Ligand/Ion
ALPHA-L-FUCOSE
4
NAG
7
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
5
SER
1
Mod. Amino Acid
SERINE
6
SO4
4
Ligand/Ion
SULFATE ION
[
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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:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TYR A:21 , ASN A:63 , ASP A:114 , NAG A:259 , FUC A:260 , HOH A:1021 , HOH A:1130
BINDING SITE FOR RESIDUE NAG A 258
02
AC2
SOFTWARE
NAG A:258 , FUC A:260
BINDING SITE FOR RESIDUE NAG A 259
03
AC3
SOFTWARE
NAG A:258 , NAG A:259 , HOH A:1199
BINDING SITE FOR RESIDUE FUC A 260
04
AC4
SOFTWARE
ASN A:71 , SER A:73 , NAG A:262 , FUC A:263
BINDING SITE FOR RESIDUE NAG A 261
05
AC5
SOFTWARE
NAG A:261 , FUC A:263
BINDING SITE FOR RESIDUE NAG A 262
06
AC6
SOFTWARE
NAG A:261 , NAG A:262
BINDING SITE FOR RESIDUE FUC A 263
07
AC7
SOFTWARE
VAL A:133 , ASN A:178 , ARG A:181 , PRO A:257 , NAG A:265 , HOH A:983 , HOH A:1057 , HOH A:1085 , HOH A:1160 , HOH A:1173 , HOH A:1193
BINDING SITE FOR RESIDUE NAG A 264
08
AC8
SOFTWARE
NAG A:264 , HOH A:1000 , HOH A:1173 , HOH A:1230
BINDING SITE FOR RESIDUE NAG A 265
09
AC9
SOFTWARE
ASN A:232 , SER A:234 , LEU A:235
BINDING SITE FOR RESIDUE NAG A 266
10
BC1
SOFTWARE
ASP A:16 , VAL A:17 , ASN A:19 , GLY A:20 , GLN A:29 , TRP A:31 , GLN A:36 , ASN A:38 , SER A:911 , HOH A:962 , HOH A:998
BINDING SITE FOR RESIDUE A2G A 267
11
BC2
SOFTWARE
THR A:4 , ARG A:37 , ARG A:40 , ASN A:151 , HOH A:1066 , HOH A:1084 , HOH A:1108 , HOH A:1119 , HOH A:1213 , HOH A:1246
BINDING SITE FOR RESIDUE SO4 A 901
12
BC3
SOFTWARE
ARG A:18 , ASN A:19 , ARG A:103 , ARG A:107 , THR A:108 , ILE A:109 , HOH A:962 , HOH A:1003 , HOH A:1228
BINDING SITE FOR RESIDUE SO4 A 902
13
BC4
SOFTWARE
THR A:161 , SER A:162 , LEU A:163 , GLN A:164 , HOH A:1056 , HOH A:1093 , HOH A:1249
BINDING SITE FOR RESIDUE SO4 A 903
14
BC5
SOFTWARE
TRP A:31 , SER A:911 , HOH A:949 , HOH A:998
BINDING SITE FOR RESIDUE SO4 A 904
15
BC6
SOFTWARE
GLU A:83 , ASP A:227 , VAL A:228 , ARG A:229 , ALA A:230 , PHE A:241 , ASN A:248 , HOH A:1009
BINDING SITE FOR RESIDUE ACT A 910
16
BC7
SOFTWARE
A2G A:267 , SO4 A:904 , HOH A:998
BINDING SITE FOR RESIDUE SER A 911
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: RICIN_B_LECTIN (-|A:129-254)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RICIN_B_LECTIN
PS50231
Lectin domain of ricin B chain profile.
NIGB_SAMNI
305-431
434-559
1
-
A:129-254
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d3ca6a1 (A:1-128)
1b: SCOP_d3ca6a2 (A:129-257)
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Protein Domains
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)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
beta-Trefoil
(385)
Superfamily
:
Ricin B-like lectins
(91)
Family
:
automated matches
(21)
Protein domain
:
automated matches
(21)
Sambucus nigra [TaxId: 4202]
(8)
1a
d3ca6a1
A:1-128
1b
d3ca6a2
A:129-257
[
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_3ca6A01 (A:1-130)
1b: CATH_3ca6A02 (A:131-255)
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Homologous Superfamilies
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)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Trefoil
(289)
Topology
:
Trefoil (Acidic Fibroblast Growth Factor, subunit A)
(289)
Homologous Superfamily
:
[code=2.80.10.50, no name defined]
(289)
European elder, elderberry (Sambucus nigra)
(8)
1a
3ca6A01
A:1-130
1b
3ca6A02
A:131-255
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Atom Selection
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Protein
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Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Asymmetric Unit 1
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select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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Asym.Unit (115 KB)
Header - Asym.Unit
Biol.Unit 1 (108 KB)
Header - Biol.Unit 1
Biol.Unit 2 (213 KB)
Header - Biol.Unit 2
Biol.Unit 3 (213 KB)
Header - Biol.Unit 3
Biol.Unit 4 (213 KB)
Header - Biol.Unit 4
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