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2JEC
Asym. Unit
Info
Asym.Unit (172 KB)
Biol.Unit 1 (164 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF RECOMBINANT DIOCLEA GRANDIFLORA LECTIN MUTANT E123A-H131N-K132Q 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
:
2.00
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Cona-Like, Metal-Binding, Legume Lectin, Carbohydrate Binding Protein, Sugar-Binding Protein
(Keyword Search:
[
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
(3, 16)
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)
2e: MANGANESE (II) ION (MNe)
2f: MANGANESE (II) ION (MNf)
2g: MANGANESE (II) ION (MNg)
2h: MANGANESE (II) ION (MNh)
3a: (2R,3S,4S,5S,6R)-2-(5-BROMO-4-CHLO... (XMMa)
3b: (2R,3S,4S,5S,6R)-2-(5-BROMO-4-CHLO... (XMMb)
3c: (2R,3S,4S,5S,6R)-2-(5-BROMO-4-CHLO... (XMMc)
3d: (2R,3S,4S,5S,6R)-2-(5-BROMO-4-CHLO... (XMMd)
View:
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Label:
No.
Name
Count
Type
Full Name
1
CA
4
Ligand/Ion
CALCIUM ION
2
MN
8
Ligand/Ion
MANGANESE (II) ION
3
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
(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
ASP A:12 , TYR A:14 , ASN A:16 , ASP A:21 , HOH A:2189 , HOH A:2207
BINDING SITE FOR RESIDUE CA A 240
02
AC2
SOFTWARE
GLU A:10 , ASP A:12 , ASP A:21 , HIS A:26 , HOH A:2216 , HOH A:2217
BINDING SITE FOR RESIDUE MN A 241
03
AC3
SOFTWARE
HIS A:53 , ASP A:194 , HOH A:2172 , HOH A:2221 , HOH A:2222 , HOH A:2223
BINDING SITE FOR RESIDUE MN A 243
04
AC4
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:2112 , HOH A:2218 , HOH A:2219 , HOH A:2220 , ILE B:31 , ASN B:85
BINDING SITE FOR RESIDUE XMM A 242
05
AC5
SOFTWARE
ASP B:12 , TYR B:14 , ASN B:16 , ASP B:21 , HOH B:2150 , HOH B:2162
BINDING SITE FOR RESIDUE CA B 240
06
AC6
SOFTWARE
GLU B:10 , ASP B:12 , ASP B:21 , HIS B:26 , HOH B:2171 , HOH B:2172
BINDING SITE FOR RESIDUE MN B 241
07
AC7
SOFTWARE
HIS B:53 , HOH B:2176
BINDING SITE FOR RESIDUE MN B 243
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:2173 , HOH B:2174 , HOH B:2175
BINDING SITE FOR RESIDUE XMM B 242
09
AC9
SOFTWARE
ASP C:12 , TYR C:14 , ASN C:16 , ASP C:21 , HOH C:2134 , HOH C:2149
BINDING SITE FOR RESIDUE CA C 240
10
BC1
SOFTWARE
GLU C:10 , ASP C:12 , ASP C:21 , HIS C:26 , HOH C:2158 , HOH C:2159
BINDING SITE FOR RESIDUE MN C 241
11
BC2
SOFTWARE
LYS B:118 , SER B:192 , HIS C:53 , ASP C:194 , HOH C:2125 , HOH C:2162
BINDING SITE FOR RESIDUE MN C 243
12
BC3
SOFTWARE
ASN A:239 , ASN C:16 , GLY C:100 , LEU C:101 , TYR C:102 , ALA C:209 , ASP C:210 , GLY C:229 , ARG C:230 , HOH C:2117 , HOH C:2160 , HOH C:2161
BINDING SITE FOR RESIDUE XMM C 242
13
BC4
SOFTWARE
ASP D:12 , TYR D:14 , ASN D:16 , ASP D:21 , HOH D:2009 , HOH D:2164
BINDING SITE FOR RESIDUE CA D 240
14
BC5
SOFTWARE
GLU D:10 , ASP D:12 , ASP D:21 , HIS D:26 , HOH D:2175 , HOH D:2176
BINDING SITE FOR RESIDUE MN D 241
15
BC6
SOFTWARE
HOH A:2171 , HIS D:53 , ASP D:194 , HOH D:2179
BINDING SITE FOR RESIDUE MN D 243
16
BC7
SOFTWARE
ARG A:35 , ASN A:239 , 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:2130 , HOH D:2177 , HOH D:2178
BINDING SITE FOR RESIDUE XMM D 242
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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)
;
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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_d2jeca_ (A:)
1b: SCOP_d2jecb_ (B:)
1c: SCOP_d2jecc_ (C:)
1d: SCOP_d2jecd_ (D:)
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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
d2jeca_
A:
1b
d2jecb_
B:
1c
d2jecc_
C:
1d
d2jecd_
D:
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_2jecA00 (A:2-239)
1b: CATH_2jecB00 (B:2-239)
1c: CATH_2jecC00 (C:2-239)
1d: CATH_2jecD00 (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
2jecA00
A:2-239
1b
2jecB00
B:2-239
1c
2jecC00
C:2-239
1d
2jecD00
D:2-239
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Pfam Domains
(1, 8)
Info
all PFAM domains
1a: PFAM_Lectin_legB_2jecD01 (D:126-239)
1b: PFAM_Lectin_legB_2jecD02 (D:126-239)
1c: PFAM_Lectin_legB_2jecD03 (D:126-239)
1d: PFAM_Lectin_legB_2jecD04 (D:126-239)
1e: PFAM_Lectin_legB_2jecD05 (D:126-239)
1f: PFAM_Lectin_legB_2jecD06 (D:126-239)
1g: PFAM_Lectin_legB_2jecD07 (D:126-239)
1h: PFAM_Lectin_legB_2jecD08 (D:126-239)
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Clan
:
Concanavalin
(293)
Family
:
Lectin_legB
(93)
Dioclea grandiflora (Mucana)
(3)
1a
Lectin_legB-2jecD01
D:126-239
1b
Lectin_legB-2jecD02
D:126-239
1c
Lectin_legB-2jecD03
D:126-239
1d
Lectin_legB-2jecD04
D:126-239
1e
Lectin_legB-2jecD05
D:126-239
1f
Lectin_legB-2jecD06
D:126-239
1g
Lectin_legB-2jecD07
D:126-239
1h
Lectin_legB-2jecD08
D:126-239
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