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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN LEGUMAIN (AEP) IN COMPLEX WITH COMPOUND 11B
 
Authors :  E. Dall, K. Ye, H. Brandstetter
Date :  08 Sep 16  (Deposition) - 29 Mar 17  (Release) - 05 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Cysteine Protease, Allosteric Inhibitor, Asparaginyl Endopeptidase, Alzheimer'S Disease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Z. Zhang, O. Obianyo, E. Dall, Y. Du, H. Fu, X. Liu, S. S. Kang, M. Song, S. P. Yu, C. Cabrele, M. Schubert, X. Li, J. Z. Wang, H. Brandstetter, K. Ye
Inhibition Of Delta-Secretase Improves Cognitive Functions In Mouse Models Of Alzheimer'S Disease.
Nat Commun V. 8 14740 2017
PubMed-ID: 28345579  |  Reference-DOI: 10.1038/NCOMMS14740

(-) Compounds

Molecule 1 - LEGUMAIN
    ChainsA, B
    EC Number3.4.22.34
    EngineeredYES
    Expression SystemLEISHMANIA TARENTOLAE
    Expression System Taxid5689
    FragmentUNP RESIDUES 26-287
    GeneLGMN, PRSC1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymASPARAGINYL ENDOPEPTIDASE,PROTEASE,CYSTEINE 1

 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  (3, 11)

Asymmetric Unit (3, 11)
No.NameCountTypeFull Name
15KN1Ligand/Ion2,4-DI(MORPHOLIN-4-YL)ANILINE
2NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
3SNN2Mod. Amino AcidL-3-AMINOSUCCINIMIDE
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
15KN-1Ligand/Ion2,4-DI(MORPHOLIN-4-YL)ANILINE
2NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
3SNN1Mod. Amino AcidL-3-AMINOSUCCINIMIDE
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
15KN1Ligand/Ion2,4-DI(MORPHOLIN-4-YL)ANILINE
2NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
3SNN1Mod. Amino AcidL-3-AMINOSUCCINIMIDE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:223 , HOH A:450 , ARG B:44 , HIS B:45 , SNN B:147 , HIS B:148 , CYS B:189 , SER B:216 , ALA B:218 , TYR B:228 , ASP B:231 , HOH B:408 , HOH B:416binding site for residue 5KN B 304
2AC2SOFTWARETYR A:76 , ASN A:91 , HOH A:401 , HOH A:431 , HOH A:440binding site for Poly-Saccharide residues NAG A 302 through NAG A 303 bound to ASN A 91
3AC3SOFTWARETYR A:71 , ASN A:167 , HIS A:171 , HOH A:457 , HOH A:465 , HOH A:472 , HOH A:496binding site for Poly-Saccharide residues NAG A 304 through NAG A 305 bound to ASN A 167
4AC4SOFTWARELYS A:181 , ASP A:200 , ASN A:201 , ASN A:272 , HOH A:467 , HOH A:522binding site for Mono-Saccharide NAG A 301 bound to ASN A 272
5AC5SOFTWAREGLU A:78 , ASN B:91 , HOH B:450binding site for Mono-Saccharide NAG B 303 bound to ASN B 91
6AC6SOFTWARELYS B:181 , ASP B:200 , ASN B:201 , ASN B:272 , HOH B:427 , HOH B:455binding site for Poly-Saccharide residues NAG B 301 through NAG B 302 bound to ASN B 272

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5LUA)

(-) 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:262
                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee...hhhhhhhhhhhhhhhhhhhhh..hhh.eeee..................................hhhhhhhhhhhhhhhhhhhhhh..............eeeeeee..ee..eee....eeehhhhhhhhhhhhhh....eeeeee...hhhhhh........eeeee.........eeeee....eeeeehhhhhhhhhhhhh.....hhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lua A  26 GGKHWVVIVAGSNGWYNYRHQADACHAYQIIHRNGIPDEQIVVMMYDDIAYSEDNPTPGIVINRPNGTDVYQGVPKDYTGEDVTPQNFLAVLRGDAEAVKGIGSGKVLKSGPQDHVFIYFTdHGSTGILVFPNEDLHVKDLNETIHYMYKHKMYRKMVFYIEACESGSMMNHLPDNINVYATTAANPRESSYACYYDEKRSTYLGDWYSVNWMEDSDVEDLTKETLHKQYHLVKSHTQTSHVMQYGNKTISTMKVMQFQGMK 287
                                    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  
                                                                                                                                                   147-SNN                                                                                                                                        

Chain B from PDB  Type:PROTEIN  Length:262
                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee...hhhhhhhhhhhhhhhhhhhh...hhh.eeee..................................hhhhhhhhhhhhhhhh.hhhhh..............eeeeeee..ee..eee....eeehhhhhhhhhhhhhh....eeeeee...hhhhhh........eeeee.........eeeee....eeeeehhhhhhhhhhhhh.....hhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lua B  26 GGKHWVVIVAGSNGWYNYRHQADACHAYQIIHRNGIPDEQIVVMMYDDIAYSEDNPTPGIVINRPNGTDVYQGVPKDYTGEDVTPQNFLAVLRGDAEAVKGIGSGKVLKSGPQDHVFIYFTdHGSTGILVFPNEDLHVKDLNETIHYMYKHKMYRKMVFYIEACESGSMMNHLPDNINVYATTAANPRESSYACYYDEKRSTYLGDWYSVNWMEDSDVEDLTKETLHKQYHLVKSHTQTSHVMQYGNKTISTMKVMQFQGMK 287
                                    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  
                                                                                                                                                   147-SNN                                                                                                                                        

   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 5LUA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (21, 21)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        LGMN_HUMAN | Q995384aw9 4awa 4awb 4fgu 4n6n 4n6o 5lu8 5lu9 5lub

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5LUA)