3VLW - JenaLib

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Biological Unit 2 (Jmol Viewer)

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
PubMed-ID: 22486720 | Reference-DOI: 10.1021/BI300194F

Molecule 1 - ALGQ1
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET3A
	Expression System Strain	:	HMS174(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 25-526
	Gene	:	ALGQ1
	Organism Scientific	:	SPHINGOMONAS SP.
	Organism Taxid	:	90322
	Strain	:	A1
	Synonym	:	ALGINATE-BINDING PROTEIN

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 24)

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

Biological Unit 1 (3, 9)

No.	Name	Count	Type	Full Name
1	BEM	1	Ligand/Ion	BETA-D-MANNURONIC ACID
2	CA	-1	Ligand/Ion	CALCIUM ION
3	GOL	7	Ligand/Ion	GLYCEROL
4	LGU	1	Ligand/Ion	ALPHA-L-GULURONATE

Biological Unit 2 (3, 13)

No.	Name	Count	Type	Full Name
1	BEM	1	Ligand/Ion	BETA-D-MANNURONIC ACID
2	CA	-1	Ligand/Ion	CALCIUM ION
3	GOL	11	Ligand/Ion	GLYCEROL
4	LGU	1	Ligand/Ion	ALPHA-L-GULURONATE

Asymmetric Unit (24, 24)

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

(no "SS Bond" information available for 3VLW)

Asymmetric Unit

No.	Residues
1	Ile A:311	-	Pro A:312
2	Ile B:311	-	Pro B:312

(no "SAP(SNP)/Variant" information available for 3VLW)

(no "PROSITE Motif" information available for 3VLW)

(no "Exon" information available for 3VLW)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:489
 aligned with Q9KWT6_SPHSX | Q9KWT6 from UniProtKB/TrEMBL  Length:526

    Alignment length:489
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505         
         Q9KWT6_SPHSX    26 EATWVTEKPLTLKIHMHFRDKWVWDENWPVAREVARLTNVKLVGVANRAATNSQEQFNLMMASGQLPDIVGGDNLKDKFIRYGMEGAFIPLNKLIDQNAPNLKAFFKTHPEVQRAITAPDGNIYYLPYVPDGLVSRGYFIRQDWLDKLHLKTPQTVDELYTVLKAFKEKDPNGNGKADEIPFINRDPEEVFRLVNFWGARSTGSNTWMDFYVENGKIKHPFAEVAFKDGIKHVAQWYKEGLIDPEIFTRKARSREQTFGNNIGGMTHDWFASTALFNDALSKNIPGFKLVPMAPPINSKGQRWEEDARQIPRPDGWAITATNKNPVETIKLFDFYFGPKGRELSNFGVPGLTYDIKNGKPVYKDTVLKAAQPVNNQMYDIGAQIPIGFWQDYEYERQWTNDVALQGIDMYIKNKYVLPQFTGVNLTVEEREIYDKYWPDVKTYMFEMGQSWVMGTKDPEKTWNDYQQQLKNRGFYQVMIVMQKAYDRQY 514
               SCOP domains d3vlwa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeeee...ee....hhhhhhhhhhhheeeee.......hhhhhhhhhhhhh....eeee..hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh........eeee......eeeeeehhhhhhh......hhhhhhhhhhhhhhh..........eee.....hhhhhhhhhhh............eee..eeehhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhh....eeeeeeehhhhhhhhhhhh.......eeee......................eeee.....hhhhhhhhhhhh.hhhhhhhhhhh.....eeee..eeeehhhhhh...hhhhhhhhh.......ee.hhhhhhh..hhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vlw A   2 EATWVTEKPLTLKIHMHFRDKWVWDENWPVAREVARLTNVKLVGVANRAATNSQEQFNLMMASGQLPDIVGGDNLKDKFIRYGMEGAFIPLNKLIDQNAPNLKAFFKTHPEVQRAITAPDGNIYYLPYVPDGLVSRGYFIRQDWLDKLHLKTPQTVDELYTVLKAFKEKDPNGNGKADEIPFINRDPEEVFRLVNFWGARSTGSNTWMDFYVENGKIKHPFAEVAFKDGIKHVAQWYKEGLIDPEIFTRKARSREQTFGNNIGGMTHDWFASTALFNDALSKNIPGFKLVPMAPPINSKGQRWEEDARQIPRPDGWAITATNKNPVETIKLFDFYFGPKGRELSNFGVPGLTYDIKNGKPVYKDTVLKAAQPVNNQMYDIGAQIPIGFWQDYEYERQWTNDVALQGIDMYIKNKYVLPQFTGVNLTVEEREIYDKYWPDVKTYMFEMGQSWVMGTKDPEKTWNDYQQQLKNRGFYQVMIVMQKAYDRQY 490
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481

Chain B from PDB  Type:PROTEIN  Length:489
 aligned with Q9KWT6_SPHSX | Q9KWT6 from UniProtKB/TrEMBL  Length:526

    Alignment length:489
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505         
         Q9KWT6_SPHSX    26 EATWVTEKPLTLKIHMHFRDKWVWDENWPVAREVARLTNVKLVGVANRAATNSQEQFNLMMASGQLPDIVGGDNLKDKFIRYGMEGAFIPLNKLIDQNAPNLKAFFKTHPEVQRAITAPDGNIYYLPYVPDGLVSRGYFIRQDWLDKLHLKTPQTVDELYTVLKAFKEKDPNGNGKADEIPFINRDPEEVFRLVNFWGARSTGSNTWMDFYVENGKIKHPFAEVAFKDGIKHVAQWYKEGLIDPEIFTRKARSREQTFGNNIGGMTHDWFASTALFNDALSKNIPGFKLVPMAPPINSKGQRWEEDARQIPRPDGWAITATNKNPVETIKLFDFYFGPKGRELSNFGVPGLTYDIKNGKPVYKDTVLKAAQPVNNQMYDIGAQIPIGFWQDYEYERQWTNDVALQGIDMYIKNKYVLPQFTGVNLTVEEREIYDKYWPDVKTYMFEMGQSWVMGTKDPEKTWNDYQQQLKNRGFYQVMIVMQKAYDRQY 514
               SCOP domains d3vlwb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeeee...ee....hhhhhhhhhhhheeeee.......hhhhhhhhhhhh.....eeee..hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh........eeee......eeeeeehhhhhhh......hhhhhhhhhhhhhhh..........eee...hhhhhhhhhhhhh............eee..eeehhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhh....eeeeeeehhhhhhhhhhhh.......eeee......................eeee.....hhhhhhhhhhhh.hhhhhhhhhhh.....eeee..eeeehhhhhh...hhhhhhhh........ee.hhhhhhh..hhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vlw B   2 EATWVTEKPLTLKIHMHFRDKWVWDENWPVAREVARLTNVKLVGVANRAATNSQEQFNLMMASGQLPDIVGGDNLKDKFIRYGMEGAFIPLNKLIDQNAPNLKAFFKTHPEVQRAITAPDGNIYYLPYVPDGLVSRGYFIRQDWLDKLHLKTPQTVDELYTVLKAFKEKDPNGNGKADEIPFINRDPEEVFRLVNFWGARSTGSNTWMDFYVENGKIKHPFAEVAFKDGIKHVAQWYKEGLIDPEIFTRKARSREQTFGNNIGGMTHDWFASTALFNDALSKNIPGFKLVPMAPPINSKGQRWEEDARQIPRPDGWAITATNKNPVETIKLFDFYFGPKGRELSNFGVPGLTYDIKNGKPVYKDTVLKAAQPVNNQMYDIGAQIPIGFWQDYEYERQWTNDVALQGIDMYIKNKYVLPQFTGVNLTVEEREIYDKYWPDVKTYMFEMGQSWVMGTKDPEKTWNDYQQQLKNRGFYQVMIVMQKAYDRQY 490
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

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:

(no "CATH Domain" information available for 3VLW)

(no "Pfam Domain" information available for 3VLW)

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q9KWT6_SPHSX | Q9KWT6)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0005215	transporter activity	Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
biological process
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.

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	Cis Peptide Bonds
		Ile A:311 - Pro A:312	[ RasMol ]
		Ile B:311 - Pro B:312	[ RasMol ]

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	3vlw
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	Q9KWT6_SPHSX \| Q9KWT6	:	1y3n 1y3p 1y3q 3a09 3vlu 3vlv

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 24)

Sites (24, 24)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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