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1NXD
Biol. Unit 3
Info
Asym.Unit (177 KB)
Biol.Unit 1 (47 KB)
Biol.Unit 2 (46 KB)
Biol.Unit 3 (46 KB)
Biol.Unit 4 (46 KB)
Biol.Unit 5 (169 KB)
Biol.Unit 6 (168 KB)
Biol.Unit 7 (88 KB)
Biol.Unit 8 (87 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF MNMN CONCANAVALIN A
Authors
:
F. J. Lopez-Jaramillo, L. A. Gonzalez-Ramirez, A. Albert, F. Santoyo- A. Vargas-Berenguel, F. Otalora
Date
:
10 Feb 03 (Deposition) - 30 Mar 04 (Release) - 05 Jul 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : 1,2,3,4
Biol. Unit 1: 1 (1x)
Biol. Unit 2: 2 (1x)
Biol. Unit 3: 3 (1x)
Biol. Unit 4: 4 (1x)
Biol. Unit 5: 1,2 (2x)
Biol. Unit 6: 3,4 (2x)
Biol. Unit 7: 1,2 (1x)
Biol. Unit 8: 3,4 (1x)
Keywords
:
Lectin, Metal Binding Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
F. J. Lopez-Jaramillo, L. A. Gonzalez-Ramirez, A. Albert, F. Santoyo-Gonzalez, A. Vargas-Berenguel, F. Otalora
Structure Of Concanavalin A At Ph 8: Bound Solvent And Crystal Contacts.
Acta Crystallogr. , Sect. D V. 60 1048 2004
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 9)
Info
All Hetero Components
1a: AZIDE ION (AZIa)
1b: AZIDE ION (AZIb)
1c: AZIDE ION (AZIc)
1d: AZIDE ION (AZId)
1e: AZIDE ION (AZIe)
1f: AZIDE ION (AZIf)
1g: AZIDE ION (AZIg)
1h: AZIDE ION (AZIh)
1i: AZIDE ION (AZIi)
1j: AZIDE ION (AZIj)
1k: AZIDE ION (AZIk)
1l: AZIDE ION (AZIl)
1m: AZIDE ION (AZIm)
1n: AZIDE ION (AZIn)
1o: AZIDE ION (AZIo)
1p: AZIDE ION (AZIp)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
2e: GLYCEROL (GOLe)
2f: GLYCEROL (GOLf)
2g: GLYCEROL (GOLg)
2h: GLYCEROL (GOLh)
2i: GLYCEROL (GOLi)
2j: GLYCEROL (GOLj)
2k: GLYCEROL (GOLk)
2l: GLYCEROL (GOLl)
2m: GLYCEROL (GOLm)
2n: GLYCEROL (GOLn)
2o: GLYCEROL (GOLo)
2p: GLYCEROL (GOLp)
2q: GLYCEROL (GOLq)
2r: GLYCEROL (GOLr)
2s: GLYCEROL (GOLs)
2t: GLYCEROL (GOLt)
2u: GLYCEROL (GOLu)
2v: GLYCEROL (GOLv)
2w: GLYCEROL (GOLw)
2x: GLYCEROL (GOLx)
2y: GLYCEROL (GOLy)
3a: MANGANESE (II) ION (MNa)
3b: MANGANESE (II) ION (MNb)
3c: MANGANESE (II) ION (MNc)
3d: MANGANESE (II) ION (MNd)
3e: MANGANESE (II) ION (MNe)
3f: MANGANESE (II) ION (MNf)
3g: MANGANESE (II) ION (MNg)
3h: MANGANESE (II) ION (MNh)
4a: SODIUM ION (NAa)
4b: SODIUM ION (NAb)
4c: SODIUM ION (NAc)
4d: SODIUM ION (NAd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AZI
4
Ligand/Ion
AZIDE ION
2
GOL
5
Ligand/Ion
GLYCEROL
3
MN
-1
Ligand/Ion
MANGANESE (II) ION
4
NA
-1
Ligand/Ion
SODIUM ION
[
close Hetero Component info
]
Sites
(16, 16)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC4 (SOFTWARE)
03: AC9 (SOFTWARE)
04: BC5 (SOFTWARE)
05: BC7 (SOFTWARE)
06: CC3 (SOFTWARE)
07: CC4 (SOFTWARE)
08: CC8 (SOFTWARE)
09: CC9 (SOFTWARE)
10: DC3 (SOFTWARE)
11: DC4 (SOFTWARE)
12: DC9 (SOFTWARE)
13: EC2 (SOFTWARE)
14: EC5 (SOFTWARE)
15: EC8 (SOFTWARE)
16: FC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER 3:110 , PHE 3:111 , THR 3:112 , HIS 3:127 , GLU 3:192 , HOH 3:1175
BINDING SITE FOR RESIDUE AZI 3 901
02
AC4
SOFTWARE
HIS 3:127 , HIS 4:127
BINDING SITE FOR RESIDUE AZI 3 904
03
AC9
SOFTWARE
GLY 3:224 , SER 3:225 , THR 3:226
BINDING SITE FOR RESIDUE AZI 3 909
04
BC5
SOFTWARE
THR 3:105 , LEU 3:198
BINDING SITE FOR RESIDUE AZI 3 914
05
BC7
SOFTWARE
HOH 3:1083 , TYR 4:12 , PRO 4:13 , GOL 4:810 , HOH 4:1081 , HOH 4:1105 , HOH 4:1135
BINDING SITE FOR RESIDUE AZI 4 916
06
CC3
SOFTWARE
ASP 3:10 , TYR 3:12 , ASN 3:14 , ASP 3:19 , HOH 3:1028 , HOH 3:1030
BINDING SITE FOR RESIDUE MN 3 1005
07
CC4
SOFTWARE
GLU 3:8 , ASP 3:10 , ASP 3:19 , HIS 3:24 , HOH 3:1029 , HOH 3:1069
BINDING SITE FOR RESIDUE MN 3 1006
08
CC8
SOFTWARE
GLU 3:122 , LEU 4:107 , ASN 4:131 , HOH 4:1078 , HOH 4:1109 , HOH 4:1141 , HOH 4:1199
BINDING SITE FOR RESIDUE NA 4 1010
09
CC9
SOFTWARE
LEU 3:107 , ASN 3:131 , HOH 3:1085 , HOH 3:1101 , HOH 3:1105 , HOH 3:1106 , GLU 4:122
BINDING SITE FOR RESIDUE NA 3 1011
10
DC3
SOFTWARE
TRP 3:88 , SER 3:113 , LYS 3:114 , ALA 3:125 , LEU 3:126 , VAL 3:179 , HIS 3:180 , HOH 3:1021 , ASP 4:139 , HOH 4:1149
BINDING SITE FOR RESIDUE GOL 3 802
11
DC4
SOFTWARE
ASN 3:14 , GLY 3:98 , LEU 3:99 , TYR 3:100 , ALA 3:207 , ASP 3:208 , ARG 3:228
BINDING SITE FOR RESIDUE GOL 3 803
12
DC9
SOFTWARE
PRO 3:86 , TRP 3:88 , ASN 3:216 , ILE 3:217 , ASP 3:218 , HOH 3:1122
BINDING SITE FOR RESIDUE GOL 3 808
13
EC2
SOFTWARE
ASN 3:44 , SER 3:201 , ASP 3:203 , PRO 4:13 , ASN 4:14 , THR 4:15 , ASP 4:16 , AZI 4:916 , HOH 4:1081 , HOH 4:1088 , HOH 4:1103
BINDING SITE FOR RESIDUE GOL 4 810
14
EC5
SOFTWARE
ASP 3:139 , HOH 3:1147 , ALA 4:125 , LEU 4:126 , PRO 4:178 , VAL 4:179 , HIS 4:180 , HOH 4:1145
BINDING SITE FOR RESIDUE GOL 4 813
15
EC8
SOFTWARE
TYR 3:54 , SER 3:56 , LYS 3:59 , ASP 3:82 , ILE 3:181 , TRP 3:182 , GLU 3:183 , ALA 3:189 , HOH 3:1152
BINDING SITE FOR RESIDUE GOL 3 816
16
FC8
SOFTWARE
LYS 3:138 , LEU 3:140 , ILE 3:141 , TYR 3:176 , HOH 3:1035 , HOH 3:1125
BINDING SITE FOR RESIDUE GOL 3 825
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
End label:
Sorry, no Info available
[
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d1nxd1_ (1:)
1b: SCOP_d1nxd2_ (2:)
1c: SCOP_d1nxd3_ (3:)
1d: SCOP_d1nxd4_ (4:)
View:
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(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
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
:
Concanavalin A
(59)
Jack bean (Canavalia ensiformis) [TaxId: 3823]
(52)
1a
d1nxd1_
1:
1b
d1nxd2_
2:
1c
d1nxd3_
3:
1d
d1nxd4_
4:
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1nxd100 (1:1-237)
1b: CATH_1nxd200 (2:1-237)
1c: CATH_1nxd300 (3:1-237)
1d: CATH_1nxd400 (4:1-237)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Jelly Rolls
(1293)
Homologous Superfamily
:
[code=2.60.120.200, no name defined]
(421)
Jack bean (Canavalia ensiformis)
(50)
1a
1nxd100
1:1-237
1b
1nxd200
2:1-237
1c
1nxd300
3:1-237
1d
1nxd400
4:1-237
[
close CATH info
]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Lectin_legB_1nxd401 (4:124-237)
1b: PFAM_Lectin_legB_1nxd402 (4:124-237)
1c: PFAM_Lectin_legB_1nxd403 (4:124-237)
1d: PFAM_Lectin_legB_1nxd404 (4:124-237)
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Select:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Concanavalin
(293)
Family
:
Lectin_legB
(93)
Canavalia ensiformis (Jack bean) (Horse bean)
(17)
1a
Lectin_legB-1nxd401
4:124-237
1b
Lectin_legB-1nxd402
4:124-237
1c
Lectin_legB-1nxd403
4:124-237
1d
Lectin_legB-1nxd404
4:124-237
[
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]
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Chain 3
Asymmetric Unit 1
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