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2JE9
Asym. Unit
Info
Asym.Unit (169 KB)
Biol.Unit 1 (162 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF RECOMBINANT DIOCLEA GRANDIFLORA LECTIN COMPLEXED WITH 5-BROMO-4-CHLORO-3-INDOLYL-A-D-MANNOSE
Authors
:
C. S. Nagano, L. Sanz, B. S. Cavada, J. J. Calvete
Date
:
16 Jan 07 (Deposition) - 30 Oct 07 (Release) - 13 Apr 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Metal-Binding, Carbohydrate Binding Protein, Cona-Like, Legume Lectin, Sugar-Binding Protein
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. S. Nagano, J. J. Calvete, D. Barettino, A. Perez, B. S. Cavada, L. San
Insights Into The Structural Basis Of The Ph- Dependent Dimer-Tetramer Equilibrium Through Crystallographic Analysis Of Recombinant Diocleinae Lectins.
Biochem. J. V. 409 417 2008
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Hetero Components
(4, 19)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
2a: MANGANESE (II) ION (MNa)
2b: MANGANESE (II) ION (MNb)
2c: MANGANESE (II) ION (MNc)
2d: MANGANESE (II) ION (MNd)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
3e: SULFATE ION (SO4e)
3f: SULFATE ION (SO4f)
3g: SULFATE ION (SO4g)
4a: (2R,3S,4S,5S,6R)-2-(5-BROMO-4-CHLO... (XMMa)
4b: (2R,3S,4S,5S,6R)-2-(5-BROMO-4-CHLO... (XMMb)
4c: (2R,3S,4S,5S,6R)-2-(5-BROMO-4-CHLO... (XMMc)
4d: (2R,3S,4S,5S,6R)-2-(5-BROMO-4-CHLO... (XMMd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
4
Ligand/Ion
CALCIUM ION
2
MN
4
Ligand/Ion
MANGANESE (II) ION
3
SO4
7
Ligand/Ion
SULFATE ION
4
XMM
4
Ligand/Ion
(2R,3S,4S,5S,6R)-2-(5-BROMO-4-CHLORO-1H-INDOL-3-YLOXY)-TETRAHYDRO-6-(HYDROXYMETHYL)-2H-PYRAN-3,4,5-TRIOL
[
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Sites
(19, 19)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:12 , TYR A:14 , ASN A:16 , ASP A:21 , HOH A:2122 , HOH A:2131
BINDING SITE FOR RESIDUE CA A1240
02
AC2
SOFTWARE
GLU A:10 , ASP A:12 , ASP A:21 , HIS A:26 , HOH A:2138 , HOH A:2139
BINDING SITE FOR RESIDUE MN A1241
03
AC3
SOFTWARE
TYR A:14 , ASN A:16 , GLY A:100 , LEU A:101 , TYR A:102 , ALA A:209 , ASP A:210 , GLY A:229 , ARG A:230 , HOH A:2140 , ILE B:31 , ASN B:85 , HOH B:2051
BINDING SITE FOR RESIDUE XMM A1242
04
AC4
SOFTWARE
SER A:136 , GLN A:137 , HOH A:2075 , HOH A:2079 , HOH A:2141 , HIS B:182
BINDING SITE FOR RESIDUE SO4 A1243
05
AC5
SOFTWARE
ALA A:40 , ARG A:41 , HOH A:2020 , HOH A:2142 , HOH A:2143 , HOH A:2144 , ASN D:23
BINDING SITE FOR RESIDUE SO4 A1244
06
AC6
SOFTWARE
ASP B:12 , TYR B:14 , ASN B:16 , ASP B:21 , HOH B:2110 , HOH B:2122
BINDING SITE FOR RESIDUE CA B1240
07
AC7
SOFTWARE
GLU B:10 , ASP B:12 , ASP B:21 , HIS B:26 , HOH B:2130 , HOH B:2131
BINDING SITE FOR RESIDUE MN B1241
08
AC8
SOFTWARE
TYR B:14 , ASN B:16 , GLY B:100 , LEU B:101 , TYR B:102 , ALA B:209 , ASP B:210 , GLY B:229 , ARG B:230 , HOH B:2132 , HOH B:2133
BINDING SITE FOR RESIDUE XMM B1242
09
AC9
SOFTWARE
HIS A:182 , GLU A:185 , HOH A:2107 , SER B:136 , GLN B:137
BINDING SITE FOR RESIDUE SO4 B1243
10
BC1
SOFTWARE
LYS B:103 , GLN B:168 , GLY B:169
BINDING SITE FOR RESIDUE SO4 B1244
11
BC2
SOFTWARE
ASN B:16 , THR B:17 , ASP B:18 , ARG B:230
BINDING SITE FOR RESIDUE SO4 B1245
12
BC3
SOFTWARE
ASP C:12 , TYR C:14 , ASN C:16 , ASP C:21 , HOH C:2066 , HOH C:2074
BINDING SITE FOR RESIDUE CA C1240
13
BC4
SOFTWARE
GLU C:10 , ASP C:12 , ASP C:21 , HIS C:26 , HOH C:2078 , HOH C:2079
BINDING SITE FOR RESIDUE MN C1241
14
BC5
SOFTWARE
TYR C:14 , ASN C:16 , GLY C:100 , LEU C:101 , TYR C:102 , ALA C:209 , ASP C:210 , ARG C:230 , XMM D:1242
BINDING SITE FOR RESIDUE XMM C1242
15
BC6
SOFTWARE
SER C:136 , GLN C:137 , HIS D:182 , GLU D:185
BINDING SITE FOR RESIDUE SO4 C1243
16
BC7
SOFTWARE
ASP D:12 , TYR D:14 , ASN D:16 , ASP D:21 , HOH D:2005 , HOH D:2077
BINDING SITE FOR RESIDUE CA D1240
17
BC8
SOFTWARE
GLU D:10 , ASP D:12 , ASP D:21 , HIS D:26 , HOH D:2082 , HOH D:2083
BINDING SITE FOR RESIDUE MN D1241
18
BC9
SOFTWARE
ARG A:35 , ASN A:239 , XMM C:1242 , TYR D:14 , ASN D:16 , GLY D:100 , LEU D:101 , TYR D:102 , ALA D:209 , ASP D:210 , GLY D:229 , ARG D:230 , HOH D:2048 , HOH D:2084 , HOH D:2085
BINDING SITE FOR RESIDUE XMM D1242
19
CC1
SOFTWARE
HIS C:182 , GLU C:185 , SER D:136 , GLN D:137
BINDING SITE FOR RESIDUE SO4 D1243
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: LECTIN_LEGUME_BETA (A:7-13,B:7-13,C:7-13,D:7-13)
2: LECTIN_LEGUME_ALPHA (A:87-96,B:87-96,C:87-96,D:87-96)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
LECTIN_LEGUME_BETA
PS00307
Legume lectins beta-chain signature.
LECA_DIOGR
5-11
4
A:7-13
B:7-13
C:7-13
D:7-13
2
LECTIN_LEGUME_ALPHA
PS00308
Legume lectins alpha-chain signature.
LECA_DIOGR
85-94
4
A:87-96
B:87-96
C:87-96
D:87-96
[
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Exons
(0, 0)
Info
All Exons
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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, 4)
Info
All SCOP Domains
1a: SCOP_d2je9a_ (A:)
1b: SCOP_d2je9b_ (B:)
1c: SCOP_d2je9c_ (C:)
1d: SCOP_d2je9d_ (D:)
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Protein Domains
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)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Concanavalin A-like lectins/glucanases
(797)
Superfamily
:
Concanavalin A-like lectins/glucanases
(797)
Family
:
Legume lectins
(238)
Protein domain
:
automated matches
(63)
Mucana (Dioclea grandiflora) [TaxId: 3837]
(2)
1a
d2je9a_
A:
1b
d2je9b_
B:
1c
d2je9c_
C:
1d
d2je9d_
D:
[
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_2je9A00 (A:2-239)
1b: CATH_2je9B00 (B:2-239)
1c: CATH_2je9C00 (C:2-239)
1d: CATH_2je9D00 (D:2-239)
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Organisms
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)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Jelly Rolls
(1293)
Homologous Superfamily
:
[code=2.60.120.200, no name defined]
(421)
Dioclea grandiflora. Organism_taxid: 3837.
(2)
1a
2je9A00
A:2-239
1b
2je9B00
B:2-239
1c
2je9C00
C:2-239
1d
2je9D00
D:2-239
[
close CATH info
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Pfam Domains
(1, 8)
Info
all PFAM domains
1a: PFAM_Lectin_legB_2je9D01 (D:126-239)
1b: PFAM_Lectin_legB_2je9D02 (D:126-239)
1c: PFAM_Lectin_legB_2je9D03 (D:126-239)
1d: PFAM_Lectin_legB_2je9D04 (D:126-239)
1e: PFAM_Lectin_legB_2je9D05 (D:126-239)
1f: PFAM_Lectin_legB_2je9D06 (D:126-239)
1g: PFAM_Lectin_legB_2je9D07 (D:126-239)
1h: PFAM_Lectin_legB_2je9D08 (D:126-239)
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Clan
:
Concanavalin
(293)
Family
:
Lectin_legB
(93)
Dioclea grandiflora (Mucana)
(3)
1a
Lectin_legB-2je9D01
D:126-239
1b
Lectin_legB-2je9D02
D:126-239
1c
Lectin_legB-2je9D03
D:126-239
1d
Lectin_legB-2je9D04
D:126-239
1e
Lectin_legB-2je9D05
D:126-239
1f
Lectin_legB-2je9D06
D:126-239
1g
Lectin_legB-2je9D07
D:126-239
1h
Lectin_legB-2je9D08
D:126-239
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