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3VLW
Asym. Unit
Info
Asym.Unit (182 KB)
Biol.Unit 1 (89 KB)
Biol.Unit 2 (91 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF SPHINGOMONAS SP. A1 ALGINATE-BINDING PROTEIN ALGQ1 IN COMPLEX WITH MANNURONATE-GULURONATE DISACCHARIDE
Authors
:
Y. Nishitani, Y. Maruyama, T. Itoh, B. Mikami, W. Hashimoto, K. Murata
Date
:
05 Dec 11 (Deposition) - 25 Jan 12 (Release) - 27 Nov 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Sugar Binding Protein, Alginate
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Nishitani, Y. Maruyama, T. Itoh, B. Mikami, W. Hashimoto, K. Murata
Recognition Of Heteropolysaccharide Alginate By Periplasmic Solute-Binding Proteins Of A Bacterial Abc Transporter
Biochemistry V. 51 3622 2012
[
close entry info
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Hetero Components
(4, 24)
Info
All Hetero Components
1a: BETA-D-MANNURONIC ACID (BEMa)
1b: BETA-D-MANNURONIC ACID (BEMb)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
3e: GLYCEROL (GOLe)
3f: GLYCEROL (GOLf)
3g: GLYCEROL (GOLg)
3h: GLYCEROL (GOLh)
3i: GLYCEROL (GOLi)
3j: GLYCEROL (GOLj)
3k: GLYCEROL (GOLk)
3l: GLYCEROL (GOLl)
3m: GLYCEROL (GOLm)
3n: GLYCEROL (GOLn)
3o: GLYCEROL (GOLo)
3p: GLYCEROL (GOLp)
3q: GLYCEROL (GOLq)
3r: GLYCEROL (GOLr)
4a: ALPHA-L-GULURONATE (LGUa)
4b: ALPHA-L-GULURONATE (LGUb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BEM
2
Ligand/Ion
BETA-D-MANNURONIC ACID
2
CA
2
Ligand/Ion
CALCIUM ION
3
GOL
18
Ligand/Ion
GLYCEROL
4
LGU
2
Ligand/Ion
ALPHA-L-GULURONATE
[
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
ASP A:171 , ASN A:173 , ASN A:175 , LYS A:177 , ASP A:179 , GLU A:180
BINDING SITE FOR RESIDUE CA A 503
02
AC2
SOFTWARE
ARG A:186 , TRP A:270 , ALA A:272 , SER A:273 , ASN A:375 , GLN A:391 , TYR A:395 , GLU A:396 , TRP A:399 , LGU A:505 , HOH A:588 , HOH A:614
BINDING SITE FOR RESIDUE BEM A 504
03
AC3
SOFTWARE
ARG A:20 , TYR A:129 , ARG A:186 , TRP A:270 , TYR A:379 , BEM A:504 , GOL A:509 , HOH A:555 , HOH A:583 , HOH A:614 , HOH A:697 , HOH A:737
BINDING SITE FOR RESIDUE LGU A 505
04
AC4
SOFTWARE
ASP A:78 , TRP A:208 , MET A:209 , ASP A:210 , TYR A:434 , TRP A:438 , LYS A:442
BINDING SITE FOR RESIDUE GOL A 506
05
AC5
SOFTWARE
ILE A:356 , LYS A:357 , ASN A:358 , GLY A:359 , LYS B:168 , LYS B:239 , GLU B:240
BINDING SITE FOR RESIDUE GOL A 507
06
AC6
SOFTWARE
ARG A:201 , GLU A:214 , GLN A:302 , TRP A:304
BINDING SITE FOR RESIDUE GOL A 508
07
AC7
SOFTWARE
ARG A:20 , ASP A:74 , ASN A:75 , ARG A:313 , ASP A:315 , LGU A:505 , HOH A:567 , HOH A:606
BINDING SITE FOR RESIDUE GOL A 509
08
AC8
SOFTWARE
GLY A:133 , LEU A:134 , VAL A:135 , HOH A:673 , HOH A:704
BINDING SITE FOR RESIDUE GOL A 510
09
AC9
SOFTWARE
ASP A:78 , LYS A:79 , ARG A:82 , ASP A:435 , HOH A:726
BINDING SITE FOR RESIDUE GOL A 511
10
BC1
SOFTWARE
LYS A:22 , TRP A:23 , ARG A:253
BINDING SITE FOR RESIDUE GOL A 512
11
BC2
SOFTWARE
ASP B:171 , ASN B:173 , ASN B:175 , LYS B:177 , ASP B:179 , GLU B:180
BINDING SITE FOR RESIDUE CA B 503
12
BC3
SOFTWARE
ARG B:186 , TRP B:270 , ALA B:272 , SER B:273 , ASN B:375 , GLN B:391 , TYR B:395 , GLU B:396 , TRP B:399 , LGU B:505 , HOH B:641 , HOH B:696
BINDING SITE FOR RESIDUE BEM B 504
13
BC4
SOFTWARE
ARG B:20 , TYR B:129 , ARG B:186 , TRP B:270 , TYR B:379 , BEM B:504 , GOL B:509 , GOL B:515 , HOH B:603 , HOH B:695 , HOH B:696 , HOH B:698 , HOH B:704
BINDING SITE FOR RESIDUE LGU B 505
14
BC5
SOFTWARE
ASP B:78 , TRP B:208 , MET B:209 , ASP B:210 , TYR B:434 , TRP B:438 , LYS B:442 , HOH B:640
BINDING SITE FOR RESIDUE GOL B 506
15
BC6
SOFTWARE
GLY B:133 , LEU B:134 , VAL B:135 , ARG B:309 , TYR B:393 , ILE B:412 , HOH B:594
BINDING SITE FOR RESIDUE GOL B 507
16
BC7
SOFTWARE
ASP B:78 , VAL B:424 , LEU B:426 , ARG B:431 , MET B:482 , HOH B:640
BINDING SITE FOR RESIDUE GOL B 508
17
BC8
SOFTWARE
LYS B:22 , ARG B:186 , ALA B:252 , LGU B:505
BINDING SITE FOR RESIDUE GOL B 509
18
BC9
SOFTWARE
GLN B:420 , PHE B:421 , THR B:422 , GLY B:423 , TYR B:486 , TYR B:490 , HOH B:597
BINDING SITE FOR RESIDUE GOL B 510
19
CC1
SOFTWARE
GLU B:189 , LYS B:251 , PHE B:446 , HOH B:567
BINDING SITE FOR RESIDUE GOL B 511
20
CC2
SOFTWARE
ARG B:33 , ALA B:36 , ARG B:37 , HOH B:719
BINDING SITE FOR RESIDUE GOL B 512
21
CC3
SOFTWARE
ALA B:223 , GLU B:224 , VAL B:225 , TYR B:476 , HOH B:521
BINDING SITE FOR RESIDUE GOL B 513
22
CC4
SOFTWARE
LYS B:232 , HIS B:233 , GLN B:236
BINDING SITE FOR RESIDUE GOL B 514
23
CC5
SOFTWARE
ARG B:20 , ASP B:74 , ASN B:75 , ARG B:313 , ASP B:315 , LGU B:505 , HOH B:575 , HOH B:603
BINDING SITE FOR RESIDUE GOL B 515
24
CC6
SOFTWARE
ALA A:3 , GLU B:447 , GLN B:450 , SER B:451 , THR B:456
BINDING SITE FOR RESIDUE GOL B 516
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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End label:
Sorry, no Info available
[
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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.
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d3vlwa_ (A:)
1b: SCOP_d3vlwb_ (B:)
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Superfamilies
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(
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Families
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Periplasmic binding protein-like II
(813)
Superfamily
:
Periplasmic binding protein-like II
(813)
Family
:
Phosphate binding protein-like
(463)
Protein domain
:
automated matches
(76)
Sphingomonas sp. [TaxId: 90322]
(5)
1a
d3vlwa_
A:
1b
d3vlwb_
B:
[
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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
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Sorry, no Info available
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Atom Selection
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Protein
Nucleic
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Sidechain
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All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
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Asymmetric Unit 1
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Example Commands
Example Command
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select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
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Asym.Unit (182 KB)
Header - Asym.Unit
Biol.Unit 1 (89 KB)
Header - Biol.Unit 1
Biol.Unit 2 (91 KB)
Header - Biol.Unit 2
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