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(-) Description

Title :  CRYSTAL STRUCTURE OF DLN1
 
Authors :  N. Jia, Y. L. Jiang, W. Cheng, H. W. Wang, C. Z. Zhou, Y. Chen
Date :  31 Aug 15  (Deposition) - 03 Feb 16  (Release) - 30 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Pore-Forming Protein, Aeolysin-Like Protein, Vetebrate, High-Mannose Glycans, Complex, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Jia, N. Liu, W. Cheng, Y. L. Jiang, H. Sun, L. L. Chen, J. Peng, Y. Zhang Y. H. Ding, Z. H. Zhang, X. Wang, G. Cai, J. Wang, M. Q. Dong, Z. Zhang, H. Wu, H. W. Wang, Y. Chen, C. Z. Zhou
Structural Basis For Receptor Recognition And Pore Formatio Of A Zebrafish Aerolysin-Like Protein.
Embo Rep. V. 17 235 2016
PubMed-ID: 26711430  |  Reference-DOI: 10.15252/EMBR.201540851

(-) Compounds

Molecule 1 - NATTERIN-LIKE PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: ZGC,113413
    Organism Common: ZEBRAFISH
    Organism Scientific: DANIO RERIO
    Organism Taxid: 7955

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 35)

Asymmetric/Biological Unit (5, 35)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2EDO12Ligand/Ion1,2-ETHANEDIOL
3PEG8Ligand/IonDI(HYDROXYETHYL)ETHER
4PG46Ligand/IonTETRAETHYLENE GLYCOL
5PGE7Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (35, 35)

Asymmetric Unit (35, 35)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL A:36 , THR A:106 , HOH A:522 , HOH A:563 , HOH A:744 , HOH A:755 , HOH A:762 , GLU B:100 , PG4 B:416 , HOH B:511binding site for residue EDO A 401
02AC2SOFTWARELEU A:7 , PEG A:408 , HOH A:511 , HOH A:547binding site for residue EDO A 402
03AC3SOFTWAREILE A:10 , GLY A:11 , TYR A:114 , EDO A:404 , CL A:418binding site for residue EDO A 403
04AC4SOFTWAREILE A:9 , GLY A:11 , GLY A:12 , EDO A:403 , EDO A:405 , PEG A:408binding site for residue EDO A 404
05AC5SOFTWAREGLY A:11 , GLN A:13 , GLY A:85 , EDO A:404binding site for residue EDO A 405
06AC6SOFTWARESER A:16 , PHE A:18 , PHE A:56 , GLY A:57 , GLY A:130 , HOH A:501 , HOH A:504 , HOH A:508 , HOH A:576 , HOH A:720binding site for residue PEG A 406
07AC7SOFTWAREGLY A:38 , TRP A:39 , SER A:107 , HOH A:506 , HOH A:554 , GLY B:109binding site for residue PEG A 407
08AC8SOFTWARESER A:17 , VAL A:127 , GLY A:128 , ARG A:129 , EDO A:402 , EDO A:404binding site for residue PEG A 408
09AC9SOFTWAREASN A:24 , ASN A:25 , ASP A:50 , ARG A:52 , HOH A:503 , HOH A:654 , HOH A:688 , HOH A:734 , THR B:157binding site for residue PEG A 409
10AD1SOFTWAREASN A:25 , GLY A:26 , SER A:49 , THR A:202 , PHE A:205 , HOH A:524binding site for residue PEG A 410
11AD2SOFTWARETHR A:167 , GLU A:222 , THR A:266 , ILE A:267 , GLY A:268 , LYS A:307 , ASN A:309 , HOH A:517 , HOH A:569binding site for residue PEG A 411
12AD3SOFTWARETHR A:5 , ASN A:6 , LEU A:7 , GLU A:8 , HOH A:547 , HOH A:606 , HOH A:727 , HOH A:779binding site for residue PGE A 412
13AD4SOFTWAREARG A:87 , GLY A:131 , SER A:132 , ASP A:133 , ASP A:135binding site for residue PGE A 413
14AD5SOFTWAREGLY A:71 , ASN A:96 , LYS A:97binding site for residue PGE A 414
15AD6SOFTWAREHIS A:104 , MET A:105 , SER A:107 , TRP A:108 , HOH A:545 , HOH A:678binding site for residue PGE A 415
16AD7SOFTWARETRP A:80 , LYS A:92 , LYS A:94 , GLU A:100 , PHE A:102 , GLU A:113 , HOH A:534binding site for residue PG4 A 416
17AD8SOFTWAREGLU A:30 , LYS A:31 , TRP A:47 , VAL A:67 , HOH A:681 , EDO B:407binding site for residue PG4 A 417
18AD9SOFTWAREGLY A:81 , GLY A:83 , GLY A:85 , EDO A:403 , HOH A:739binding site for residue CL A 418
19AE1SOFTWAREPHE B:18 , VAL B:127 , GLY B:128binding site for residue EDO B 401
20AE2SOFTWAREILE B:10 , GLY B:11 , EDO B:403 , CL B:417binding site for residue EDO B 402
21AE3SOFTWAREGLY B:11 , GLN B:13 , EDO B:402 , HOH B:867binding site for residue EDO B 403
22AE4SOFTWAREGLU B:184 , HOH B:545 , HOH B:620 , HOH B:862binding site for residue EDO B 404
23AE5SOFTWAREASN B:25 , SER B:49 , ASP B:50 , THR B:202 , HOH B:506 , HOH B:818binding site for residue EDO B 405
24AE6SOFTWARETHR A:69 , PG4 B:414binding site for residue EDO B 406
25AE7SOFTWAREPG4 A:417 , THR B:69 , GLU B:72 , LYS B:97 , HOH B:580 , HOH B:617binding site for residue EDO B 407
26AE8SOFTWARETHR B:5 , ASN B:6 , LEU B:7 , GLU B:8 , HOH B:504 , HOH B:609binding site for residue PEG B 408
27AE9SOFTWARETHR B:167 , THR B:266 , ILE B:267 , GLY B:268 , LYS B:307 , HOH B:517 , HOH B:772binding site for residue PEG B 409
28AF1SOFTWARESER B:16 , PHE B:18 , GLU B:54 , PHE B:56 , GLY B:57 , GLY B:130 , HOH B:547binding site for residue PGE B 410
29AF2SOFTWAREHIS B:104 , MET B:105 , SER B:107 , TRP B:108 , HOH B:744 , HOH B:775binding site for residue PGE B 411
30AF3SOFTWARESER A:107 , HOH A:584 , TRP B:39 , TRP B:108 , HOH B:648 , HOH B:754 , HOH B:771binding site for residue PGE B 412
31AF4SOFTWAREARG B:87 , GLY B:131 , SER B:132 , ASP B:133 , ASP B:135 , HOH B:549 , HOH B:769binding site for residue PG4 B 413
32AF5SOFTWARELYS B:31 , TRP B:47 , EDO B:406 , HOH B:654 , HOH B:675binding site for residue PG4 B 414
33AF6SOFTWARELYS A:191 , PRO B:70 , ASN B:96 , LYS B:97 , HOH B:580binding site for residue PG4 B 415
34AF7SOFTWAREEDO A:401 , SER B:76 , LEU B:77 , TRP B:80 , LYS B:92 , LYS B:94 , GLU B:100 , PHE B:102 , GLU B:113binding site for residue PG4 B 416
35AF8SOFTWAREGLY B:81 , ASN B:82 , GLY B:83 , GLY B:85 , EDO B:402 , HOH B:845binding site for residue CL B 417

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5DI0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5DI0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DI0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DI0)

(-) Exons   (0, 0)

(no "Exon" information available for 5DI0)

(-) 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:318
                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eee..ee....eeeeee.......eeeeeeee....eeeeeeee....eeeee......eeee......eeeeeeee......eeeeeeee....eeeee........eeee......eeeeeeee...eeeeeeeee..eeeeeeeeee..........eeeeeeeeeeeee.....eeeeeeeeeeeeeeeee..hhhhhhhh.eeeee..eeeee....eeeee...eeee.eeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeeeeeeeeeee....eeeeeeeeeeeeeee...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5di0 A  -2 GSHMTYPTNLEIIGGQGGSSFSFTGENNGASLEKIWVWVGGWQIKAVRAWLSDGRDETFGVPSGSHQEYVFTPGECFTSLSLWGNGAGTRLGAIKFKTNKGGEFFAHMTSWGLKTEYPMDVGSGYCLGIVGRGGSDIDCMGFMFLNAVQSTVLTNVNYPTINQLIPKVATEEIKSVSFENKTSVKQEQKVETSKKVIKTSSWSMTKSFSSTFSVEVSAGIPEIAEVSTGFSISFGVESTHSLEQTDEKNETLTTTVEVPPKKKVDVHITIGRASFDLPYTGTVKITCKNGSVLQYETKGQYKGVAYTDIKVNTVEKDL 315
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307        


Chain B from PDB  Type:PROTEIN  Length:318
                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......ee...ee....eeeeee.......eeeeeeee....eeeeeeee....eeeee......eeee......eeeeeeee......eeeeeeee....eeeee........eeee......eeeeeeee...eeeeeeeee..eeeeeeeeee..........eeeeeeeeeeeee.....eeeeeeeeeeeeeeeee..hhhhhhhh.eeeee..eeeeee..eeeeee...eeee.eeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeeeeeeeeeee....eeeeeeeeeeeeeee...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5di0 B  -2 GSHMTYPTNLEIIGGQGGSSFSFTGENNGASLEKIWVWVGGWQIKAVRAWLSDGRDETFGVPSGSHQEYVFTPGECFTSLSLWGNGAGTRLGAIKFKTNKGGEFFAHMTSWGLKTEYPMDVGSGYCLGIVGRGGSDIDCMGFMFLNAVQSTVLTNVNYPTINQLIPKVATEEIKSVSFENKTSVKQEQKVETSKKVIKTSSWSMTKSFSSTFSVEVSAGIPEIAEVSTGFSISFGVESTHSLEQTDEKNETLTTTVEVPPKKKVDVHITIGRASFDLPYTGTVKITCKNGSVLQYETKGQYKGVAYTDIKVNTVEKDL 315
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307
   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)

(no "SCOP Domain" information available for 5DI0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DI0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DI0)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        NATTL_DANRE | Q5CZR5: 4zno 4znq 4znr

(-) Related Entries Specified in the PDB File

4zno