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3VKL
Biol. Unit 2
Info
Asym.Unit (108 KB)
Biol.Unit 1 (53 KB)
Biol.Unit 2 (53 KB)
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(1)
Title
:
PROTEASE-RESISTANT MUTANT FORM OF HUMAN GALECTIN-8 IN COMPLEX WITH TWO LACTOSE MOLECULES
Authors
:
S. Kamitori, H. Yoshida
Date
:
18 Nov 11 (Deposition) - 12 Sep 12 (Release) - 03 Jul 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.55
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Beta-Sandwich, Carbohydrate Binding, Oligosaccharide, Sugar Binding Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Yoshida, S. Yamashita, M. Teraoka, A. Itoh, S. Nakakita, N. Nishi, S. Kamitori
X-Ray Structure Of A Protease-Resistant Mutant Form Of Huma Galectin-8 With Two Carbohydrate Recognition Domains
Febs J. V. 279 3937 2012
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Hetero Components
(3, 12)
Info
All Hetero Components
1a: BETA-D-GLUCOSE (BGCa)
1b: BETA-D-GLUCOSE (BGCb)
1c: BETA-D-GLUCOSE (BGCc)
1d: BETA-D-GLUCOSE (BGCd)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
2f: 1,2-ETHANEDIOL (EDOf)
2g: 1,2-ETHANEDIOL (EDOg)
2h: 1,2-ETHANEDIOL (EDOh)
2i: 1,2-ETHANEDIOL (EDOi)
2j: 1,2-ETHANEDIOL (EDOj)
2k: 1,2-ETHANEDIOL (EDOk)
2l: 1,2-ETHANEDIOL (EDOl)
2m: 1,2-ETHANEDIOL (EDOm)
2n: 1,2-ETHANEDIOL (EDOn)
2o: 1,2-ETHANEDIOL (EDOo)
2p: 1,2-ETHANEDIOL (EDOp)
2q: 1,2-ETHANEDIOL (EDOq)
2r: 1,2-ETHANEDIOL (EDOr)
2s: 1,2-ETHANEDIOL (EDOs)
2t: 1,2-ETHANEDIOL (EDOt)
3a: BETA-D-GALACTOSE (GALa)
3b: BETA-D-GALACTOSE (GALb)
3c: BETA-D-GALACTOSE (GALc)
3d: BETA-D-GALACTOSE (GALd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BGC
2
Ligand/Ion
BETA-D-GLUCOSE
2
EDO
8
Ligand/Ion
1,2-ETHANEDIOL
3
GAL
2
Ligand/Ion
BETA-D-GALACTOSE
[
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Sites
(13, 13)
Info
All Sites
01: AC4 (SOFTWARE)
02: AC6 (SOFTWARE)
03: BC8 (SOFTWARE)
04: BC9 (SOFTWARE)
05: CC1 (SOFTWARE)
06: CC2 (SOFTWARE)
07: CC3 (SOFTWARE)
08: CC4 (SOFTWARE)
09: CC5 (SOFTWARE)
10: CC6 (SOFTWARE)
11: CC7 (SOFTWARE)
12: CC8 (SOFTWARE)
13: CC9 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC4
SOFTWARE
ARG A:233 , GLU A:252 , ARG A:254 , GAL A:403 , SER B:248
BINDING SITE FOR RESIDUE BGC A 404
02
AC6
SOFTWARE
GLN A:115 , ALA A:117 , HIS A:122 , MET B:265 , ASN B:283
BINDING SITE FOR RESIDUE EDO A 406
03
BC8
SOFTWARE
ARG B:45 , HIS B:65 , ASN B:67 , ARG B:69 , VAL B:77 , ASN B:79 , TRP B:86 , GLU B:89 , BGC B:402 , HOH B:551 , HOH B:554
BINDING SITE FOR RESIDUE GAL B 401
04
BC9
SOFTWARE
ARG B:69 , GLU B:89 , GAL B:401 , EDO B:410 , HOH B:551
BINDING SITE FOR RESIDUE BGC B 402
05
CC1
SOFTWARE
HIS B:229 , ASN B:231 , ARG B:233 , ASN B:242 , TRP B:249 , GLU B:252 , BGC B:404
BINDING SITE FOR RESIDUE GAL B 403
06
CC2
SOFTWARE
GLU A:251 , ARG B:233 , GLU B:252 , ARG B:254 , GAL B:403 , HOH B:589
BINDING SITE FOR RESIDUE BGC B 404
07
CC3
SOFTWARE
GLU B:90 , LEU B:125 , TYR B:126 , GLY B:127 , EDO B:409 , HOH B:502 , HOH B:541
BINDING SITE FOR RESIDUE EDO B 405
08
CC4
SOFTWARE
SER B:102 , ASN B:119
BINDING SITE FOR RESIDUE EDO B 406
09
CC5
SOFTWARE
ILE A:91 , TYR A:93 , ILE B:12 , PHE B:19 , THR B:22
BINDING SITE FOR RESIDUE EDO B 407
10
CC6
SOFTWARE
HIS B:147 , LEU B:234 , LYS B:237 , PRO B:263
BINDING SITE FOR RESIDUE EDO B 408
11
CC7
SOFTWARE
HOH A:564 , THR B:92 , THR B:123 , LEU B:124 , LEU B:125 , EDO B:405
BINDING SITE FOR RESIDUE EDO B 409
12
CC8
SOFTWARE
GLN A:9 , ASN A:10 , ARG A:184 , GLY B:87 , GLU B:89 , BGC B:402
BINDING SITE FOR RESIDUE EDO B 410
13
CC9
SOFTWARE
ARG B:315 , HOH B:575
BINDING SITE FOR RESIDUE EDO B 412
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SAPs(SNPs)/Variants
(4, 4)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_012990 (F19Y, chain B, )
2: VAR_009710 (R36C, chain B, )
3: VAR_012991 (M56V, chain B, )
4: VAR_063506 (R184S, chain B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_012990
F
19
Y
LEG8_HUMAN
Polymorphism
2737713
B
F
19
Y
2
UniProt
VAR_009710
R
36
C
LEG8_HUMAN
Polymorphism
1041935
B
R
36
C
3
UniProt
VAR_012991
M
56
V
LEG8_HUMAN
Polymorphism
1041937
B
M
56
V
4
UniProt
VAR_063506
R
184
S
LEG8_HUMAN
Polymorphism
2243525
B
R
184
S
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: GALECTIN (B:187-317)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
GALECTIN
PS51304
Galactoside-binding lectin (galectin) domain profile.
LEG8_HUMAN
19-152
187-317
2
-
B:19-152
-
B:187-317
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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_d3vkla1 (A:3-154)
1b: SCOP_d3vkla2 (A:155-317)
1c: SCOP_d3vklb1 (B:3-154)
1d: SCOP_d3vklb2 (B:155-317)
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Protein Domains
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Organisms
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Class
:
All beta proteins
(24004)
Fold
:
Concanavalin A-like lectins/glucanases
(797)
Superfamily
:
Concanavalin A-like lectins/glucanases
(797)
Family
:
automated matches
(133)
Protein domain
:
automated matches
(133)
Human (Homo sapiens) [TaxId: 9606]
(36)
1a
d3vkla1
A:3-154
1b
d3vkla2
A:155-317
1c
d3vklb1
B:3-154
1d
d3vklb2
B:155-317
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Label:
Sorry, no Info available
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Protein & NOT Variant
Protein & NOT Site
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Chain B
Asymmetric Unit 1
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select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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select non-helix/non-sheet protein parts
set fontsize 20
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show SS bonds with a radius of 100 units (=0.4Å)
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