4QFP - JenaLib

Title :   CRYSTAL STRUCTURE OF DIPEPTIDE BINDING PROTEIN FROM PSEUDOALTEROMONAS SP. SM9913 IN COMPLEX WITH VAL-THR

Authors :   C. Y. Li, Y. Z. Zhang

Date :   21 May 14 (Deposition) - 28 Jan 15 (Release) - 28 Jan 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Dipeptide Binding Protein, Peptide Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Y. Li, Y. Z. Zhang
Structural Insights Into The Multispecific Recognition Of Dipeptides Of Deep-Sea Gram-Negative Bacterium Pseudoalteromonas Sp. Strain Sm9913
J. Bacteriol. 2015
PubMed: search

Compounds

Molecule 1 - ABC TRANSPORTER PERIPLASMIC PEPTIDE-BINDING PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	DPPA
	Organism Scientific	:	PSEUDOALTEROMONAS
	Organism Taxid	:	234831
	Strain	:	SM9913
	Synonym	:	PERIPLASMIC DIPEPTIDE-BINDING PROTEIN

Structural Features

Chains, Units

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

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (4, 8)

Asymmetric Unit (4, 8)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	PO4	2	Ligand/Ion	PHOSPHATE ION
3	THR	2	Mod. Amino Acid	THREONINE
4	VAL	2	Mod. Amino Acid	VALINE

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL
2	PO4	1	Ligand/Ion	PHOSPHATE ION
3	THR	1	Mod. Amino Acid	THREONINE
4	VAL	1	Mod. Amino Acid	VALINE

Biological Unit 2 (4, 5)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	PO4	1	Ligand/Ion	PHOSPHATE ION
3	THR	1	Mod. Amino Acid	THREONINE
4	VAL	1	Mod. Amino Acid	VALINE

Sites (6, 6)

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:364 , GLY A:367 , TYR A:368 , GLU A:369 , HOH A:849 , LYS B:97 , SER B:159 , ASP B:160 , HIS B:161	BINDING SITE FOR RESIDUE PO4 A 603
2	AC2	SOFTWARE	LYS B:234 , ASN B:531 , HOH B:871 , HOH B:872 , HOH B:1039 , HOH B:1087	BINDING SITE FOR RESIDUE PO4 B 603
3	AC3	SOFTWARE	TYR B:33 , ALA B:266 , HIS B:267 , PRO B:268 , ILE B:384 , ARG B:508 , PHE B:509 , GLN B:510 , ILE B:527 , HOH B:748	BINDING SITE FOR RESIDUE GOL B 604
4	AC4	SOFTWARE	THR B:288 , ASN B:289 , LEU B:332 , HIS B:505 , GLY B:506 , MET B:507	BINDING SITE FOR RESIDUE GOL B 605
5	AC5	SOFTWARE	THR A:48 , THR A:49 , GLY A:50 , PHE A:182 , ARG A:383 , TYR A:385 , TRP A:433 , ALA A:434 , ASP A:436 , HOH A:704	BINDING SITE FOR LINKED RESIDUES A 601 to 602
6	AC6	SOFTWARE	THR B:48 , THR B:49 , GLY B:50 , ARG B:383 , TYR B:385 , TRP B:433 , ALA B:434 , ASP B:436 , HOH B:717 , HOH B:953	BINDING SITE FOR LINKED RESIDUES B 601 to 602

SS Bonds (4, 4)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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:509
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.......hhhhh.hhhhhhhhhhhhh...eee......eee..eeeeee.....eeeeee..................hhhhhhhhhhh...............hhhhhhhhhhh.eeeeeeee..eeeeee.....hhhhhhh.......hhhhhhhhhhhhhhhhh.........eeeeeee...eeeeee............eeeeee..hhhhhhhhhhh....eee..hhhhhhhhhhh..eeeeee...eeeeeee........hhhhhhhhhh..hhhhhhhhh.....ee.....................hhhhhhhhhhhhh....eeeeee..........hhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhh....eeeeeee....hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.eeeeee..eeeeee..ee...............ee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qfp A  29 QGLVYCAEANPVSFNPQVTTTGSTIDIIANQLYDRLISIDPVTAEFKSELATDWKISKDGKSVTFTLRKGVKFHTTAYFTPTREFNADDVIFTFSRLFDVYNPYHFVGDANYPYFQSVGIDQLIRKIVRVSDHQVRFELFNAESSFLANMATDFAVVLSKEYAMALKANNQENLFDQYPVGTGPYIYKEYRRDHLVRFYKNADYWKHEVALEQLVYDITPNGTTRIAKILTKECDVTAHPSSAQLSILAQRDDINVERETNLNIGYWAFNTERPPFDNLKVRQALVHAIDIEKIMQAVYYGNGLRARSILPPTSWAFEPQKNMPIFDPQLAKKLLTEAGYEKGFDMSIWAMPVSRIYNPNARKMAELMQSDLRKIGVNVNIVEYEWNTFIQRIGEHRHDSVLLGWAADTPDPDNFFSPLLSCTATFSGKNPANWCNPEFDLLLTKALDTTDLNLRKQYYDAAQSMIIEQLPLYPIAHGMRFQASSADVEGITLGPFGAISLANARKKVT 602
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528      || 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    535| 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     601

Chain B from PDB  Type:PROTEIN  Length:509
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.......hhhhh.hhhhhhhhhhhhh...eee......eee..eeeeee.....eeeeee..................hhhhhhhhhhhhhh............hhhhhhhhhhh.eeeeeeee..eeeeee.....hhhhhh........hhhhhhhhhhhhhhhhh.........eeeeeee...eeeeee............eeeeee..hhhhhhhhhhh....eee..hhhhhhhhhhh..eeeeee...eeeeeee........hhhhhhhhhh..hhhhhhhhh.....ee.....................hhhhhhhhhhh......eeeeeee.........hhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhh....eeeeeee....hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.eeeeee..eeeeee..ee...............ee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qfp B  29 QGLVYCAEANPVSFNPQVTTTGSTIDIIANQLYDRLISIDPVTAEFKSELATDWKISKDGKSVTFTLRKGVKFHTTAYFTPTREFNADDVIFTFSRLFDVYNPYHFVGDANYPYFQSVGIDQLIRKIVRVSDHQVRFELFNAESSFLANMATDFAVVLSKEYAMALKANNQENLFDQYPVGTGPYIYKEYRRDHLVRFYKNADYWKHEVALEQLVYDITPNGTTRIAKILTKECDVTAHPSSAQLSILAQRDDINVERETNLNIGYWAFNTERPPFDNLKVRQALVHAIDIEKIMQAVYYGNGLRARSILPPTSWAFEPQKNMPIFDPQLAKKLLTEAGYEKGFDMSIWAMPVSRIYNPNARKMAELMQSDLRKIGVNVNIVEYEWNTFIQRIGEHRHDSVLLGWAADTPDPDNFFSPLLSCTATFSGKNPANWCNPEFDLLLTKALDTTDLNLRKQYYDAAQSMIIEQLPLYPIAHGMRFQASSADVEGITLGPFGAISLANARKKVT 602
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528      || 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    535| 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     601

Legend:		→ Mismatch	(orange background)
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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (2, 2)

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	Cis Peptide Bonds
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