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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN DPP-IV IN COMPLEX WITH HL1
 
Authors :  F. Wu, H. Li, Z. Zhao, L. Zhu, H. Xu, S. Li
Date :  31 Mar 16  (Deposition) - 05 Apr 17  (Release) - 05 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.75
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Human Dpp-Iv, Protease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. Wu, H. Li, Z. Zhao, L. Zhu, H. Xu, S. Li
Crystal Structure Of Human Dpp-Iv In Complex With Hl1
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DIPEPTIDYL PEPTIDASE 4
    ChainsA, B
    EC Number3.4.14.5
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Taxid7108
    Expression System Vector TypePLASMID
    GeneDPP4, ADCP2, CD26
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymADABP,ADENOSINE DEAMINASE COMPLEXING PROTEIN 2,ADCP-2, DIPEPTIDYL PEPTIDASE IV,DPP IV,T-CELL ACTIVATION ANTIGEN CD26,TP103

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1HL12Ligand/Ion(2~{S},3~{R})-8,9-DIMETHOXY-3-[2,4,5-TRIS(FLUORANYL)PHENYL]-2,3-DIHYDRO-1~{H}-BENZO[F]CHROMEN-2-AMINE
2MAN3Ligand/IonALPHA-D-MANNOSE
3NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:125 , GLU A:205 , GLU A:206 , SER A:209 , PHE A:357 , ARG A:358 , TYR A:547 , SER A:630 , TYR A:631 , VAL A:656 , TYR A:662 , TYR A:666 , ASN A:710 , VAL A:711 , HIS A:740binding site for residue HL1 A 801
2AC2SOFTWAREARG B:125 , GLU B:205 , GLU B:206 , VAL B:207 , SER B:209 , PHE B:357 , ARG B:358 , TYR B:547 , SER B:630 , TYR B:631 , VAL B:656 , TYR B:662 , TYR B:666 , ASN B:710 , VAL B:711binding site for residue HL1 B 801
3AC3SOFTWAREASN A:229 , THR A:231 , GLU A:232 , LYS A:267binding site for Mono-Saccharide NAG A 802 bound to ASN A 229
4AC4SOFTWARESER A:690 , ILE B:194 , ASN B:229 , GLU B:232 , LYS B:267binding site for Poly-Saccharide residues NAG B 803 through MAN B 806 bound to ASN B 229
5AC5SOFTWAREVAL B:279 , ASN B:281 , HOH B:901binding site for Mono-Saccharide NAG B 802 bound to ASN B 281

(-) SS Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1A:328 -A:339
2A:385 -A:394
3A:444 -A:447
4A:454 -A:472
5A:649 -A:762
6B:328 -B:339
7B:385 -B:394
8B:444 -B:447
9B:454 -B:472
10B:649 -B:762

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:474 -Pro A:475
2Gly B:474 -Pro B:475

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5J3J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5J3J)

(-) Exons   (0, 0)

(no "Exon" information available for 5J3J)

(-) Sequences/Alignments

Asymmetric/Biological 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:727
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.hhhhhhhh........eee....eeeeee..eeeeee.....eeeee...........eeeeee.....eeeeeeeeee.....eeeeeeeee....ee...........eeee......eeeee..eeeee.......ee.........eee...hhhhhhhh......eee.....eeeeeeee.....eeeeee.........eeeeee.........eeeeeeee............ee...hhhhhh..eeeeeeeeee..eeeeeeee....eeeeeeeeee....eeee.hhhheeee.............eee.....eeeeeee.....eeeeeee......ee.......eeeeeee...eeeeee.hhhhh....eeeeee..eeeeeee............eeeee.....eeeeee......eeeeee....eeeeeee.hhhhhhhh..ee..eeeeeeeee..eeeeeeeee.........eeeeeee...............hhhhhhhhh...eeeee........hhhhhhhhh....hhhhhhhhhhhhhhhh...eeeeeeeeeeehhhhhhhhhhhh.......eeeee....hhhhhhhhhhhhhhh......hhhhhhhh.hhhhhhhhhhheeeeeee......hhhhhhhhhhhhhhh....eeeee........hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j3j A  40 RKTYTLTDYLKNTYRLKLYSLRWISDHEYLYKQENNILVFNAEYGNSSVFLENSTFDEFGHSINDYSISPDGQFILLEYNYVKQWRHSYTASYDIYDLNKRQLITEERIPNNTQWVTWSPVGHKLAYVWNNDIYVKIEPNLPSYRITWTGKEDIIYNGITDWVYEEEVFSAYSALWWSPNGTFLAYAQFNDTEVPLIEYSFYSDESLQYPKTVRVPYPKAGAVNPTVKFFVVNTDSLSSVTNATSIQITAPASMLIGDHYLCDVTWATQERISLQWLRRIQNYSVMDICDYDESSGRWNCLVARQHIEMSTTGWVGRFRPSEPHFTLDGNSFYKIISNEEGYRHICYFQIDKKDCTFITKGTWEVIGIEALTSDYLYYISNEYKGMPGGRNLYKIQLSDYTKVTCLSCELNPERCQYYSVSFSKEAKYYQLRCSGPGLPLYTLHSSVNDKGLRVLEDNSALDKMLQNVQMPSKKLDFIILNETKFWYQMILPPHFDKSKKYPLLLDVYAGPCSQKADTVFRLNWATYLASTENIIVASFDGRGSGYQGDKIMHAINRRLGTFEVEDQIEAARQFSKMGFVDNKRIAIWGWSYGGYVTSMVLGSGSGVFKCGIAVAPVSRWEYYDSVYTERYMGLPTPEDNLDHYRNSTVMSRAENFKQVEYLLIHGTADDNVHFQQSAQISKALVDVGVDFQAMWYTDEDHGIASSTAHQHIYTHMSHFIKQCFSLP 766
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       

Chain B from PDB  Type:PROTEIN  Length:727
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhh..........ee....eeeeee..eeeeee......eeeehhhhhh.....eeeeee......eeeeeeeee.....eeeeeeee..................eeee......eeeee..eeeee.......ee.........eee...hhhhhhhh......eee.....eeeeeeee.....eeeeee.........eeeeee.........eeeeeeee............ee...hhhhhh..eeeeeeee....eeeeeeee....eeeeeeeee......eee.hhhheeee..............ee.....eeeeeee.....eeeeeee..eeeeee.......eeeeeee...eeeeee.hhhhh....eeeeee......eee.........eeeeeeee.....eeeeeeeee...eeeeee....eeeeeee.hhhhhhhhh.......eeeeeee..eeeeeeee..........eeeeeee...............hhhhhhhhh...eeeee........hhhhhhhhh....hhhhhhhhhhhhhhhhh..eeeeeeeeeeehhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhheeeeeee......hhhhhhhhhhhhhhh....eeeee........hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j3j B  40 RKTYTLTDYLKNTYRLKLYSLRWISDHEYLYKQENNILVFNAEYGNSSVFLENSTFDEFGHSINDYSISPDGQFILLEYNYVKQWRHSYTASYDIYDLNKRQLITEERIPNNTQWVTWSPVGHKLAYVWNNDIYVKIEPNLPSYRITWTGKEDIIYNGITDWVYEEEVFSAYSALWWSPNGTFLAYAQFNDTEVPLIEYSFYSDESLQYPKTVRVPYPKAGAVNPTVKFFVVNTDSLSSVTNATSIQITAPASMLIGDHYLCDVTWATQERISLQWLRRIQNYSVMDICDYDESSGRWNCLVARQHIEMSTTGWVGRFRPSEPHFTLDGNSFYKIISNEEGYRHICYFQIDKKDCTFITKGTWEVIGIEALTSDYLYYISNEYKGMPGGRNLYKIQLSDYTKVTCLSCELNPERCQYYSVSFSKEAKYYQLRCSGPGLPLYTLHSSVNDKGLRVLEDNSALDKMLQNVQMPSKKLDFIILNETKFWYQMILPPHFDKSKKYPLLLDVYAGPCSQKADTVFRLNWATYLASTENIIVASFDGRGSGYQGDKIMHAINRRLGTFEVEDQIEAARQFSKMGFVDNKRIAIWGWSYGGYVTSMVLGSGSGVFKCGIAVAPVSRWEYYDSVYTERYMGLPTPEDNLDHYRNSTVMSRAENFKQVEYLLIHGTADDNVHFQQSAQISKALVDVGVDFQAMWYTDEDHGIASSTAHQHIYTHMSHFIKQCFSLP 766
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       

   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 5J3J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5J3J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5J3J)

(-) Gene Ontology  (42, 42)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gly A:474 - Pro A:475   [ RasMol ]  
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        DPP4_HUMAN | P274871j2e 1n1m 1nu6 1nu8 1pfq 1r9m 1r9n 1rwq 1tk3 1tkr 1u8e 1w1i 1wcy 1x70 2ajl 2bgn 2bgr 2bub 2fjp 2g5p 2g5t 2g63 2hha 2i03 2i78 2iit 2iiv 2jid 2oag 2ogz 2ole 2onc 2oph 2oqi 2oqv 2p8s 2qjr 2qky 2qoe 2qt9 2qtb 2rgu 2rip 3bjm 3c43 3c45 3ccb 3ccc 3d4l 3eio 3f8s 3g0b 3g0c 3g0d 3g0g 3h0c 3hab 3hac 3kwf 3kwj 3nox 3o95 3o9v 3oc0 3opm 3q0t 3q8w 3qbj 3sww 3sx4 3vjk 3vjl 3vjm 3w2t 3wqh 4a5s 4dsa 4dsz 4dtc 4g1f 4j3j 4jh0 4kr0 4l72 4lko 4n8d 4n8e 4pnz 4pv7 4qzv 5i7u 5ism 5kby 5t4b 5t4e 5t4f 5t4h

(-) Related Entries Specified in the PDB File

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