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1NXD
Biol. Unit 7
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, 22)
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
8
Ligand/Ion
AZIDE ION
2
GOL
14
Ligand/Ion
GLYCEROL
3
MN
-1
Ligand/Ion
MANGANESE (II) ION
4
NA
-1
Ligand/Ion
SODIUM ION
[
close Hetero Component info
]
Sites
(30, 30)
Info
All Sites
01: AC2 (SOFTWARE)
02: AC3 (SOFTWARE)
03: AC5 (SOFTWARE)
04: AC7 (SOFTWARE)
05: AC8 (SOFTWARE)
06: BC1 (SOFTWARE)
07: BC3 (SOFTWARE)
08: BC4 (SOFTWARE)
09: BC6 (SOFTWARE)
10: BC8 (SOFTWARE)
11: BC9 (SOFTWARE)
12: CC1 (SOFTWARE)
13: CC2 (SOFTWARE)
14: CC7 (SOFTWARE)
15: DC1 (SOFTWARE)
16: DC5 (SOFTWARE)
17: DC7 (SOFTWARE)
18: DC8 (SOFTWARE)
19: EC1 (SOFTWARE)
20: EC3 (SOFTWARE)
21: EC4 (SOFTWARE)
22: EC6 (SOFTWARE)
23: EC7 (SOFTWARE)
24: EC9 (SOFTWARE)
25: FC1 (SOFTWARE)
26: FC3 (SOFTWARE)
27: FC4 (SOFTWARE)
28: FC5 (SOFTWARE)
29: FC6 (SOFTWARE)
30: FC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC2
SOFTWARE
HIS 2:127 , HOH 2:1055
BINDING SITE FOR RESIDUE AZI 2 902
02
AC3
SOFTWARE
HOH 1:1133 , ASP 4:218 , SER 4:220
BINDING SITE FOR RESIDUE AZI 4 903
03
AC5
SOFTWARE
LYS 2:138 , LEU 2:140 , TYR 2:176
BINDING SITE FOR RESIDUE AZI 2 905
04
AC7
SOFTWARE
THR 1:105 , GLU 1:155 , HOH 1:1093 , HOH 1:1184
BINDING SITE FOR RESIDUE AZI 1 907
05
AC8
SOFTWARE
GOL 1:804 , TYR 2:12 , PRO 2:13 , HIS 2:205 , HOH 2:1029 , HOH 2:1119
BINDING SITE FOR RESIDUE AZI 2 908
06
BC1
SOFTWARE
SER 1:113 , LYS 1:114 , HIS 1:180 , ILE 1:181 , SER 1:190 , PHE 1:191 , GOL 1:812 , HOH 1:1110
BINDING SITE FOR RESIDUE AZI 1 910
07
BC3
SOFTWARE
SER 1:110 , PHE 1:111 , THR 1:112 , GLU 1:192 , ALA 1:193 , THR 1:194
BINDING SITE FOR RESIDUE AZI 1 912
08
BC4
SOFTWARE
TRP 1:88 , ASN 1:124 , HIS 1:180 , GOL 1:812 , PHE 2:130 , GLN 2:137 , ASP 2:139 , HOH 2:1160
BINDING SITE FOR RESIDUE AZI 2 913
09
BC6
SOFTWARE
THR 2:103 , THR 2:105 , GLU 2:155 , LYS 2:200 , HOH 2:1168
BINDING SITE FOR RESIDUE AZI 2 915
10
BC8
SOFTWARE
ASP 1:10 , TYR 1:12 , ASN 1:14 , ASP 1:19 , HOH 1:1062 , HOH 1:1063
BINDING SITE FOR RESIDUE MN 1 1001
11
BC9
SOFTWARE
GLU 1:8 , ASP 1:10 , ASP 1:19 , HIS 1:24 , HOH 1:1064 , HOH 1:1116
BINDING SITE FOR RESIDUE MN 1 1002
12
CC1
SOFTWARE
ASP 2:10 , TYR 2:12 , ASN 2:14 , ASP 2:19 , HOH 2:1014 , HOH 2:1046
BINDING SITE FOR RESIDUE MN 2 1003
13
CC2
SOFTWARE
GLU 2:8 , ASP 2:10 , ASP 2:19 , HIS 2:24 , HOH 2:1035 , HOH 2:1092
BINDING SITE FOR RESIDUE MN 2 1004
14
CC7
SOFTWARE
LEU 2:107 , ASN 2:131 , HOH 2:1096 , HOH 2:1135 , HOH 2:1167
BINDING SITE FOR RESIDUE NA 2 1009
15
DC1
SOFTWARE
LEU 1:107 , ASN 1:131 , HOH 1:1147 , HOH 1:1151 , GLU 2:122 , HOH 2:1116 , HOH 2:1131
BINDING SITE FOR RESIDUE NA 1 1012
16
DC5
SOFTWARE
ASN 1:44 , SER 1:201 , ASP 1:203 , SER 1:204 , HOH 1:1097 , HOH 1:1145 , PRO 2:13 , ASN 2:14 , THR 2:15 , ASP 2:16 , GOL 2:815 , AZI 2:908 , HOH 2:1094
BINDING SITE FOR RESIDUE GOL 1 804
17
DC7
SOFTWARE
PRO 1:222 , SER 1:223 , PRO 1:234 , HOH 1:1032 , HOH 1:1081 , SER 4:168 , HOH 4:1095
BINDING SITE FOR RESIDUE GOL 1 806
18
DC8
SOFTWARE
ASN 1:14 , GLY 1:98 , LEU 1:99 , TYR 1:100 , ALA 1:207 , ASP 1:208 , ARG 1:228 , HOH 1:1027
BINDING SITE FOR RESIDUE GOL 1 807
19
EC1
SOFTWARE
ALA 2:38 , LYS 2:39 , SER 2:72 , ALA 2:73 , THR 2:74 , HOH 2:1144 , HOH 2:1192
BINDING SITE FOR RESIDUE GOL 2 809
20
EC3
SOFTWARE
SER 2:113 , LEU 2:115 , LEU 2:126 , PRO 2:178 , VAL 2:179 , HIS 2:180 , HOH 2:1024 , HOH 2:1045
BINDING SITE FOR RESIDUE GOL 2 811
21
EC4
SOFTWARE
SER 1:113 , ASN 1:124 , ALA 1:125 , VAL 1:179 , HIS 1:180 , AZI 1:910 , HOH 1:1059 , HOH 1:1225 , AZI 2:913
BINDING SITE FOR RESIDUE GOL 1 812
22
EC6
SOFTWARE
ASN 2:14 , GLY 2:98 , LEU 2:99 , TYR 2:100 , ALA 2:207 , ASP 2:208 , ARG 2:228 , GOL 2:815 , HOH 2:1050
BINDING SITE FOR RESIDUE GOL 2 814
23
EC7
SOFTWARE
TYR 1:100 , SER 1:204 , HIS 1:205 , GOL 1:804 , TYR 2:12 , LEU 2:99 , GOL 2:814
BINDING SITE FOR RESIDUE GOL 2 815
24
EC9
SOFTWARE
VAL 1:170 , GLY 1:224 , HOH 1:1126 , HOH 1:1207 , GOL 4:819 , HOH 4:1030
BINDING SITE FOR RESIDUE GOL 4 817
25
FC1
SOFTWARE
GLN 2:143 , GLY 2:144 , SER 2:220 , ILE 2:221 , HOH 2:1012
BINDING SITE FOR RESIDUE GOL 2 818
26
FC3
SOFTWARE
ARG 2:228 , PRO 2:234 , ASP 2:235 , ALA 2:236 , HOH 2:1132
BINDING SITE FOR RESIDUE GOL 2 820
27
FC4
SOFTWARE
TYR 1:12 , PRO 1:13 , ASN 1:14 , THR 1:15 , ASP 1:16 , HOH 1:1015 , LEU 2:99
BINDING SITE FOR RESIDUE GOL 1 821
28
FC5
SOFTWARE
GLN 1:143 , GLY 1:144 , SER 1:220 , ILE 1:221
BINDING SITE FOR RESIDUE GOL 1 822
29
FC6
SOFTWARE
SER 1:72 , ALA 1:73 , THR 1:74
BINDING SITE FOR RESIDUE GOL 1 823
30
FC7
SOFTWARE
LYS 1:138 , LEU 1:140 , ILE 1:141 , TYR 1:176 , HOH 1:1107 , HOH 1:1155 , HOH 1:1165 , HOH 1:1198
BINDING SITE FOR RESIDUE GOL 1 824
[
close Site info
]
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:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
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Select:
Label:
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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(
)
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(
)
(
)
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:
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Label:
Classes
(
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(
)
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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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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Asym.Unit (177 KB)
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Header - Biol.Unit 1
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