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(-) Description

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

  12
Asymmetric Unit : AB
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.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2PO42Ligand/IonPHOSPHATE ION
3THR2Mod. Amino AcidTHREONINE
4VAL2Mod. Amino AcidVALINE
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2PO41Ligand/IonPHOSPHATE ION
3THR1Mod. Amino AcidTHREONINE
4VAL1Mod. Amino AcidVALINE
Biological Unit 2 (4, 5)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2PO41Ligand/IonPHOSPHATE ION
3THR1Mod. Amino AcidTHREONINE
4VAL1Mod. Amino AcidVALINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR 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:161BINDING SITE FOR RESIDUE PO4 A 603
2AC2SOFTWARELYS B:234 , ASN B:531 , HOH B:871 , HOH B:872 , HOH B:1039 , HOH B:1087BINDING SITE FOR RESIDUE PO4 B 603
3AC3SOFTWARETYR 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:748BINDING SITE FOR RESIDUE GOL B 604
4AC4SOFTWARETHR B:288 , ASN B:289 , LEU B:332 , HIS B:505 , GLY B:506 , MET B:507BINDING SITE FOR RESIDUE GOL B 605
5AC5SOFTWARETHR 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:704BINDING SITE FOR LINKED RESIDUES A 601 to 602
6AC6SOFTWARETHR 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:953BINDING SITE FOR LINKED RESIDUES B 601 to 602

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:34 -A:262
2A:450 -A:463
3B:34 -B:262
4B:450 -B:463

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Pro A:302 -Pro A:303
2Pro B:302 -Pro B:303
3Ala B:366 -Gly B:367

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4QFP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4QFP)

(-) Exons   (0, 0)

(no "Exon" information available for 4QFP)

(-) 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)
  - → 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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4QFP)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4QFP)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4QFP)

(-) Gene Ontology  (2, 2)

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(-) Related Entries Specified in the PDB File

4qfk 4qfl 4qfn 4qfo