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2X3T
Asym. Unit
Info
Asym.Unit (212 KB)
Biol.Unit 1 (104 KB)
Biol.Unit 2 (103 KB)
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(1)
Title
:
GLUTARALDEHYDE-CROSSLINKED WHEAT GERM AGGLUTININ ISOLECTIN 1 CRYSTAL SOAKED WITH A SYNTHETIC GLYCOPEPTIDE
Authors
:
D. Schwefel, C. Maierhofer, V. Wittmann, K. Diederichs, W. Welte
Date
:
26 Jan 10 (Deposition) - 30 Jun 10 (Release) - 28 Dec 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.75
Chains
:
Asym. Unit : A,B,C,D,E,M
Biol. Unit 1: C,D,M (1x)
Biol. Unit 2: A,B,E (1x)
Keywords
:
Sugar Binding Protein-Peptide Complex, Chitin-Binding
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. Schwefel, C. Maierhofer, J. G. Beck, S. Seeberger, K. Diederichs, H. M. Moller, W. Welte, V. Wittmann
Structural Basis Of Multivalent Binding To Wheat Germ Agglutinin.
J. Am. Chem. Soc. V. 132 8704 2010
[
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Hetero Components
(4, 27)
Info
All Hetero Components
1a: D-ALPHA-AMINOBUTYRIC ACID (DBBa)
1b: D-ALPHA-AMINOBUTYRIC ACID (DBBb)
1c: D-ALPHA-AMINOBUTYRIC ACID (DBBc)
1d: D-ALPHA-AMINOBUTYRIC ACID (DBBd)
1e: D-ALPHA-AMINOBUTYRIC ACID (DBBe)
1f: D-ALPHA-AMINOBUTYRIC ACID (DBBf)
1g: D-ALPHA-AMINOBUTYRIC ACID (DBBg)
1h: D-ALPHA-AMINOBUTYRIC ACID (DBBh)
1i: D-ALPHA-AMINOBUTYRIC ACID (DBBi)
1j: D-ALPHA-AMINOBUTYRIC ACID (DBBj)
1k: D-ALPHA-AMINOBUTYRIC ACID (DBBk)
2a: GLYCEROLGLYCERIN; PROPANE-1,2,3-TR... (GOLa)
2b: GLYCEROLGLYCERIN; PROPANE-1,2,3-TR... (GOLb)
2c: GLYCEROLGLYCERIN; PROPANE-1,2,3-TR... (GOLc)
3a: 2-(ACETYLAMINO)-1-O-CARBAMOYL-2-DE... (GYVa)
3b: 2-(ACETYLAMINO)-1-O-CARBAMOYL-2-DE... (GYVb)
3c: 2-(ACETYLAMINO)-1-O-CARBAMOYL-2-DE... (GYVc)
3d: 2-(ACETYLAMINO)-1-O-CARBAMOYL-2-DE... (GYVd)
3e: 2-(ACETYLAMINO)-1-O-CARBAMOYL-2-DE... (GYVe)
3f: 2-(ACETYLAMINO)-1-O-CARBAMOYL-2-DE... (GYVf)
3g: 2-(ACETYLAMINO)-1-O-CARBAMOYL-2-DE... (GYVg)
3h: 2-(ACETYLAMINO)-1-O-CARBAMOYL-2-DE... (GYVh)
3i: 2-(ACETYLAMINO)-1-O-CARBAMOYL-2-DE... (GYVi)
3j: 2-(ACETYLAMINO)-1-O-CARBAMOYL-2-DE... (GYVj)
3k: 2-(ACETYLAMINO)-1-O-CARBAMOYL-2-DE... (GYVk)
4a: PYROGLUTAMIC ACID (PCAa)
4b: PYROGLUTAMIC ACID (PCAb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DBB
11
Mod. Amino Acid
D-ALPHA-AMINOBUTYRIC ACID
2
GOL
3
Ligand/Ion
GLYCEROLGLYCERIN; PROPANE-1,2,3-TRIOL
3
GYV
11
Ligand/Ion
2-(ACETYLAMINO)-1-O-CARBAMOYL-2-DEOXY-ALPHA-D-GLUCOPYRANOSE
4
PCA
2
Mod. Amino Acid
PYROGLUTAMIC ACID
[
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]
Sites
(21, 21)
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)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:72 , ASP B:86 , SER B:105 , TRP B:107 , PHE B:109 , HOH B:2004 , DBB E:4
BINDING SITE FOR RESIDUE GYV E1004
02
AC2
SOFTWARE
SER A:62 , TYR A:64 , TYR A:66 , GLU A:72 , TYR A:73 , SER B:114 , GLU B:115 , DBB E:5
BINDING SITE FOR RESIDUE GYV E1005
03
AC3
SOFTWARE
ASP A:86 , SER A:105 , TRP A:107 , PHE A:109 , GLU A:115 , DBB A:1171 , ALA B:71 , GLU B:72
BINDING SITE FOR RESIDUE GYV A1170
04
AC4
SOFTWARE
GYV A:1170
BINDING SITE FOR RESIDUE DBB A1171
05
AC5
SOFTWARE
ASP A:129 , SER A:148 , TRP A:150 , SER A:152 , GLY A:158 , TYR A:159 , DBB A:1173 , ASP B:29
BINDING SITE FOR RESIDUE GYV A1172
06
AC6
SOFTWARE
GYV A:1172
BINDING SITE FOR RESIDUE DBB A1173
07
AC7
SOFTWARE
PRO A:157 , SER B:19 , TYR B:21 , TYR B:23 , ASP B:29 , TYR B:30 , DBB B:1171
BINDING SITE FOR RESIDUE GYV B1170
08
AC8
SOFTWARE
GYV B:1170
BINDING SITE FOR RESIDUE DBB B1171
09
AC9
SOFTWARE
GLU A:115 , SER B:62 , TYR B:66 , GLU B:72 , TYR B:73 , DBB B:1173
BINDING SITE FOR RESIDUE GYV B1172
10
BC1
SOFTWARE
GYV B:1172
BINDING SITE FOR RESIDUE DBB B1173
11
BC2
SOFTWARE
GLY A:124 , ALA A:125 , CYS A:126 , ASP A:129 , CYS A:153 , MET B:26
BINDING SITE FOR RESIDUE GOL A1174
12
BC3
SOFTWARE
MET A:26 , GLY A:27 , TRP A:41 , ALA B:125 , CYS B:126 , THR B:128 , ASP B:129 , TYR B:145
BINDING SITE FOR RESIDUE GOL B1174
13
BC4
SOFTWARE
SER C:62 , TYR C:66 , GLU C:72 , TYR C:73 , SER D:114 , GLU D:115 , DBB M:4
BINDING SITE FOR RESIDUE GYV M1004
14
BC5
SOFTWARE
GLU C:72 , ASP D:86 , SER D:105 , TRP D:107 , PHE D:109 , DBB M:5
BINDING SITE FOR RESIDUE GYV M1005
15
BC6
SOFTWARE
ASP C:86 , SER C:105 , TRP C:107 , PHE C:109 , GLU C:115 , PHE C:116 , DBB C:1173 , HOH C:2012 , ALA D:71 , GLU D:72
BINDING SITE FOR RESIDUE GYV C1172
16
BC7
SOFTWARE
GYV C:1172
BINDING SITE FOR RESIDUE DBB C1173
17
BC8
SOFTWARE
PRO C:157 , TYR D:21 , TYR D:23 , ASP D:29 , TYR D:30 , DBB D:1171
BINDING SITE FOR RESIDUE GYV D1170
18
BC9
SOFTWARE
GYV D:1170
BINDING SITE FOR RESIDUE DBB D1171
19
CC1
SOFTWARE
SER C:114 , GLU C:115 , SER D:62 , TYR D:66 , GLU D:72 , TYR D:73 , DBB D:1173
BINDING SITE FOR RESIDUE GYV D1172
20
CC2
SOFTWARE
GYV D:1172
BINDING SITE FOR RESIDUE DBB D1173
21
CC3
SOFTWARE
MET C:26 , GLY C:27 , TRP C:41 , ALA D:125 , CYS D:126 , THR D:128 , ASP D:129 , CYS D:153
BINDING SITE FOR RESIDUE GOL D1176
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(2, 28)
Info
All PROSITE Patterns/Profiles
1: CHIT_BIND_I_2 (-|A:43-85,B:43-85,C:43-85,D:43-85|...)
2: CHIT_BIND_I_1 (A:12-31,B:12-31,C:12-31,D:12-31|A:...)
;
View:
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Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
CHIT_BIND_I_2
PS50941
Chitin-binding type-1 domain profile.
AGI1_WHEAT
26-68
69-111
112-154
155-197
12
-
A:43-85
B:43-85
C:43-85
D:43-85
A:86-128
B:86-128
C:86-128
D:86-128
A:129-170
B:129-170
C:129-170
D:129-171
2
CHIT_BIND_I_1
PS00026
Chitin recognition or binding domain signature.
AGI1_WHEAT
38-57
81-100
124-143
167-186
16
A:12-31
B:12-31
C:12-31
D:12-31
A:55-74
B:55-74
C:55-74
D:55-74
A:98-117
B:98-117
C:98-117
D:98-117
A:141-160
B:141-160
C:141-160
D:141-160
[
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Exons
(0, 0)
Info
All Exons
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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.
SCOP Domains
(1, 16)
Info
All SCOP Domains
1a: SCOP_d2x3ta1 (A:1-52)
1b: SCOP_d2x3tb1 (B:3-52)
1c: SCOP_d2x3tb2 (B:53-86)
1d: SCOP_d2x3tb3 (B:87-129)
1e: SCOP_d2x3tb4 (B:130-170)
1f: SCOP_d2x3tc1 (C:2-52)
1g: SCOP_d2x3tc2 (C:53-86)
1h: SCOP_d2x3tc3 (C:87-129)
1i: SCOP_d2x3tc4 (C:130-170)
1j: SCOP_d2x3td1 (D:1-52)
1k: SCOP_d2x3td2 (D:53-86)
1l: SCOP_d2x3td3 (D:87-129)
1m: SCOP_d2x3td4 (D:130-171)
1n: SCOP_d2x3ta2 (A:53-86)
1o: SCOP_d2x3ta3 (A:87-129)
1p: SCOP_d2x3ta4 (A:130-170)
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Classes
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)
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)
(
)
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)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Small proteins
(3458)
Fold
:
Knottins (small inhibitors, toxins, lectins)
(761)
Superfamily
:
Plant lectins/antimicrobial peptides
(31)
Family
:
Hevein-like agglutinin (lectin) domain
(28)
Protein domain
:
Wheat germ agglutinin (WGA)
(12)
Wheat (Triticum aestivum), also known as Triticum vulgare [TaxId: 4565]
(12)
1a
d2x3ta1
A:1-52
1b
d2x3tb1
B:3-52
1c
d2x3tb2
B:53-86
1d
d2x3tb3
B:87-129
1e
d2x3tb4
B:130-170
1f
d2x3tc1
C:2-52
1g
d2x3tc2
C:53-86
1h
d2x3tc3
C:87-129
1i
d2x3tc4
C:130-170
1j
d2x3td1
D:1-52
1k
d2x3td2
D:53-86
1l
d2x3td3
D:87-129
1m
d2x3td4
D:130-171
1n
d2x3ta2
A:53-86
1o
d2x3ta3
A:87-129
1p
d2x3ta4
A:130-170
[
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CATH Domains
(1, 12)
Info
all CATH domains
1a: CATH_2x3tA04 (A:129-170)
1b: CATH_2x3tA02 (A:43-85)
1c: CATH_2x3tB02 (B:43-85)
1d: CATH_2x3tC02 (C:43-85)
1e: CATH_2x3tD02 (D:43-85)
1f: CATH_2x3tA03 (A:86-128)
1g: CATH_2x3tB03 (B:86-128)
1h: CATH_2x3tC03 (C:86-128)
1i: CATH_2x3tD03 (D:86-128)
1j: CATH_2x3tB04 (B:129-170)
1k: CATH_2x3tD04 (D:129-171)
1l: CATH_2x3tC04 (C:129-170)
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Topologies
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)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Wheat Germ Agglutinin (Isolectin 2); domain 1
(140)
Homologous Superfamily
:
[code=3.30.60.10, no name defined]
(23)
Wheat (Triticum aestivum)
(2)
1a
2x3tA04
A:129-170
1b
2x3tA02
A:43-85
1c
2x3tB02
B:43-85
1d
2x3tC02
C:43-85
1e
2x3tD02
D:43-85
1f
2x3tA03
A:86-128
1g
2x3tB03
B:86-128
1h
2x3tC03
C:86-128
1i
2x3tD03
D:86-128
1j
2x3tB04
B:129-170
1k
2x3tD04
D:129-171
1l
2x3tC04
C:129-170
[
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Pfam Domains
(1, 16)
Info
all PFAM domains
1a: PFAM_Chitin_bind_1_2x3tD01 (D:129-169)
1b: PFAM_Chitin_bind_1_2x3tD02 (D:129-169)
1c: PFAM_Chitin_bind_1_2x3tD03 (D:129-169)
1d: PFAM_Chitin_bind_1_2x3tD04 (D:129-169)
1e: PFAM_Chitin_bind_1_2x3tD05 (D:129-169)
1f: PFAM_Chitin_bind_1_2x3tD06 (D:129-169)
1g: PFAM_Chitin_bind_1_2x3tD07 (D:129-169)
1h: PFAM_Chitin_bind_1_2x3tD08 (D:129-169)
1i: PFAM_Chitin_bind_1_2x3tD09 (D:129-169)
1j: PFAM_Chitin_bind_1_2x3tD10 (D:129-169)
1k: PFAM_Chitin_bind_1_2x3tD11 (D:129-169)
1l: PFAM_Chitin_bind_1_2x3tD12 (D:129-169)
1m: PFAM_Chitin_bind_1_2x3tD13 (D:129-169)
1n: PFAM_Chitin_bind_1_2x3tD14 (D:129-169)
1o: PFAM_Chitin_bind_1_2x3tD15 (D:129-169)
1p: PFAM_Chitin_bind_1_2x3tD16 (D:129-169)
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Families
(
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(
)
Organisms
(
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(
)
Clan
:
no clan defined [family: Chitin_bind_1]
(17)
Family
:
Chitin_bind_1
(17)
Triticum aestivum (Wheat)
(8)
1a
Chitin_bind_1-2x3tD01
D:129-169
1b
Chitin_bind_1-2x3tD02
D:129-169
1c
Chitin_bind_1-2x3tD03
D:129-169
1d
Chitin_bind_1-2x3tD04
D:129-169
1e
Chitin_bind_1-2x3tD05
D:129-169
1f
Chitin_bind_1-2x3tD06
D:129-169
1g
Chitin_bind_1-2x3tD07
D:129-169
1h
Chitin_bind_1-2x3tD08
D:129-169
1i
Chitin_bind_1-2x3tD09
D:129-169
1j
Chitin_bind_1-2x3tD10
D:129-169
1k
Chitin_bind_1-2x3tD11
D:129-169
1l
Chitin_bind_1-2x3tD12
D:129-169
1m
Chitin_bind_1-2x3tD13
D:129-169
1n
Chitin_bind_1-2x3tD14
D:129-169
1o
Chitin_bind_1-2x3tD15
D:129-169
1p
Chitin_bind_1-2x3tD16
D:129-169
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