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3D4K
Biol. Unit 1
Info
Asym.Unit (170 KB)
Biol.Unit 1 (163 KB)
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(1)
Title
:
CONCANAVALIN A COMPLEXED TO A SYNTHETIC ANALOG OF THE TRIMANNOSIDE
Authors
:
R. Kadirvelraj, B. L. Foley, J. D. Dyekjaer, R. J. Woods
Date
:
14 May 08 (Deposition) - 03 Mar 09 (Release) - 07 Jun 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Concanavalin A, Conserved Water, Carbohydrate-Protein Binding, Glycoprotein, Lectin, Manganese, Metal-Binding, Sugar Binding Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. Kadirvelraj, B. L. Foley, J. D. Dyekjaer, R. J. Woods
Involvement Of Water In Carbohydrate-Protein Binding: Concanavalin A Revisited.
J. Am. Chem. Soc. V. 130 16933 2008
(for further references see the
PDB file header
)
[
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Hetero Components
(3, 8)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
2c: GLYCEROL (GOLc)
2d: GLYCEROL (GOLd)
3a: METHYL 2-DEOXY-2-(2-HYDROXYETHYL)-... (H1Ma)
3b: METHYL 2-DEOXY-2-(2-HYDROXYETHYL)-... (H1Mb)
3c: METHYL 2-DEOXY-2-(2-HYDROXYETHYL)-... (H1Mc)
3d: METHYL 2-DEOXY-2-(2-HYDROXYETHYL)-... (H1Md)
4a: ALPHA-D-MANNOSE (MANa)
4b: ALPHA-D-MANNOSE (MANb)
4c: ALPHA-D-MANNOSE (MANc)
4d: ALPHA-D-MANNOSE (MANd)
4e: ALPHA-D-MANNOSE (MANe)
4f: ALPHA-D-MANNOSE (MANf)
4g: ALPHA-D-MANNOSE (MANg)
4h: ALPHA-D-MANNOSE (MANh)
5a: MANGANESE (II) ION (MNa)
5b: MANGANESE (II) ION (MNb)
5c: MANGANESE (II) ION (MNc)
5d: MANGANESE (II) ION (MNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
GOL
2
Ligand/Ion
GLYCEROL
3
H1M
2
Ligand/Ion
METHYL 2-DEOXY-2-(2-HYDROXYETHYL)-ALPHA-D-MANNOPYRANOSIDE
4
MAN
4
Ligand/Ion
ALPHA-D-MANNOSE
5
MN
-1
Ligand/Ion
MANGANESE (II) ION
[
close Hetero Component info
]
Sites
(24, 24)
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)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:14 , GLY A:98 , LEU A:99 , TYR A:100 , ALA A:207 , ASP A:208 , ARG A:228 , HOH A:368 , HOH A:765
BINDING SITE FOR RESIDUE MAN A 240
02
AC2
SOFTWARE
TYR A:12 , PRO A:13 , ASN A:14 , THR A:15 , ASP A:16
BINDING SITE FOR RESIDUE MAN A 242
03
AC3
SOFTWARE
TYR B:12 , ASN B:14 , GLY B:98 , LEU B:99 , TYR B:100 , ALA B:207 , ASP B:208 , GLY B:227 , ARG B:228 , HOH B:280 , HOH B:367
BINDING SITE FOR RESIDUE MAN B 240
04
AC4
SOFTWARE
TYR B:12 , PRO B:13 , ASN B:14 , THR B:15 , ASP B:16 , HOH B:720
BINDING SITE FOR RESIDUE MAN B 242
05
AC5
SOFTWARE
ASN C:14 , GLY C:98 , LEU C:99 , TYR C:100 , ALA C:207 , ASP C:208 , ARG C:228 , HOH C:370 , HOH C:371 , HOH C:742
BINDING SITE FOR RESIDUE MAN C 240
06
AC6
SOFTWARE
TYR C:12 , PRO C:13 , ASN C:14 , THR C:15 , ASP C:16
BINDING SITE FOR RESIDUE MAN C 242
07
AC7
SOFTWARE
TYR D:12 , ASN D:14 , GLY D:98 , LEU D:99 , TYR D:100 , ALA D:207 , ASP D:208 , ARG D:228 , HOH D:290 , HOH D:312
BINDING SITE FOR RESIDUE MAN D 240
08
AC8
SOFTWARE
TYR D:12 , PRO D:13 , ASN D:14 , THR D:15 , ASP D:16
BINDING SITE FOR RESIDUE MAN D 242
09
AC9
SOFTWARE
GLU A:8 , ASP A:10 , ASP A:19 , HIS A:24 , HOH A:307 , HOH A:365
BINDING SITE FOR RESIDUE MN A 238
10
BC1
SOFTWARE
ASP A:10 , TYR A:12 , ASN A:14 , ASP A:19 , HOH A:250 , HOH A:447
BINDING SITE FOR RESIDUE CA A 239
11
BC2
SOFTWARE
GLU B:8 , ASP B:10 , ASP B:19 , HIS B:24 , HOH B:264 , HOH B:306
BINDING SITE FOR RESIDUE MN B 238
12
BC3
SOFTWARE
ASP B:10 , TYR B:12 , ASN B:14 , ASP B:19 , HOH B:257 , HOH B:444
BINDING SITE FOR RESIDUE CA B 239
13
BC4
SOFTWARE
GLU C:8 , ASP C:10 , ASP C:19 , HIS C:24 , HOH C:256 , HOH C:386
BINDING SITE FOR RESIDUE MN C 238
14
BC5
SOFTWARE
ASP C:10 , TYR C:12 , ASN C:14 , ASP C:19 , HOH C:281 , HOH C:449
BINDING SITE FOR RESIDUE CA C 239
15
BC6
SOFTWARE
GLU D:8 , ASP D:10 , ASP D:19 , HIS D:24 , HOH D:270 , HOH D:271
BINDING SITE FOR RESIDUE MN D 238
16
BC7
SOFTWARE
ASP D:10 , TYR D:12 , ASN D:14 , ASP D:19 , HOH D:253 , HOH D:445
BINDING SITE FOR RESIDUE CA D 239
17
BC8
SOFTWARE
TYR A:12 , ASP A:16 , LEU A:99 , TYR A:100 , ARG A:228 , HOH A:390 , HOH A:759
BINDING SITE FOR RESIDUE H1M A 241
18
BC9
SOFTWARE
TYR B:12 , ASP B:16 , ARG B:228 , HOH B:279 , HOH B:423
BINDING SITE FOR RESIDUE H1M B 241
19
CC1
SOFTWARE
TYR C:12 , ASP C:16 , LEU C:99 , ARG C:228 , HOH C:448
BINDING SITE FOR RESIDUE H1M C 241
20
CC2
SOFTWARE
TYR D:12 , ASP D:16 , LEU D:99 , ARG D:228 , HOH D:297 , HOH D:315 , HOH D:580
BINDING SITE FOR RESIDUE H1M D 241
21
CC3
SOFTWARE
PHE A:130 , ASP A:139 , HOH A:330 , SER D:113 , HIS D:180 , HOH D:509
BINDING SITE FOR RESIDUE GOL D 900
22
CC4
SOFTWARE
ASP B:139 , HOH B:291 , SER C:113 , HIS C:180 , HOH C:717
BINDING SITE FOR RESIDUE GOL C 900
23
CC5
SOFTWARE
SER B:113 , HIS B:180 , PHE C:130 , GLN C:137 , ASP C:139 , HOH C:296
BINDING SITE FOR RESIDUE GOL B 900
24
CC6
SOFTWARE
SER A:113 , ASN A:124 , HIS A:180 , HOH A:309 , PHE D:130 , GLN D:137 , ASP D:139 , HOH D:413
BINDING SITE FOR RESIDUE GOL A 900
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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PROSITE Patterns/Profiles
(, 0)
Info
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;
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d3d4ka_ (A:)
1b: SCOP_d3d4kb_ (B:)
1c: SCOP_d3d4kc_ (C:)
1d: SCOP_d3d4kd_ (D:)
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(
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(
)
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
d3d4ka_
A:
1b
d3d4kb_
B:
1c
d3d4kc_
C:
1d
d3d4kd_
D:
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_3d4kA00 (A:1-237)
1b: CATH_3d4kB00 (B:1-237)
1c: CATH_3d4kC00 (C:1-237)
1d: CATH_3d4kD00 (D:1-237)
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(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Jelly Rolls
(1293)
Homologous Superfamily
:
[code=2.60.120.200, no name defined]
(421)
Horse bean (Canavalia ensiformis)
(1)
1a
3d4kA00
A:1-237
1b
3d4kB00
B:1-237
1c
3d4kC00
C:1-237
1d
3d4kD00
D:1-237
[
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]
Pfam Domains
(0, 0)
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all PFAM domains
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