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(-) Description

Title :  CRYSTAL STRUCTURE OF YVAD-CMK BOUND 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 :  1.95
Chains :  Asym./Biol. Unit :  A,C
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 - AC-TYR-VAL-ALA-ASP-CHLOROMETHYLKETONE
    Chains: C
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 2 - LEGUMAIN
    Chains: A
    EC Number: 3.4.22.34
    Engineered: YES
    Expression System: LEISHMANIA TARENTOLAE
    Expression System Taxid: 5689
    Fragment: UNP RESIDUES 26-288
    Gene: LGMN, PRSC1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ASPARAGINYL ENDOPEPTIDASE,PROTEASE,CYSTEINE 1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 9)

Asymmetric/Biological Unit (7, 9)
No.NameCountTypeFull Name
10QE1Mod. Amino AcidCHLOROMETHANE
25KN1Ligand/Ion2,4-DI(MORPHOLIN-4-YL)ANILINE
3ACE1Mod. Amino AcidACETYL GROUP
4EMC1Ligand/IonETHYL MERCURY ION
5NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
6SNN1Mod. Amino AcidL-3-AMINOSUCCINIMIDE
7SO42Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:58 , ASN A:91 , LYS A:224 , ARG A:225 , HOH A:430binding site for residue SO4 A 301
2AC2SOFTWARETHR A:250 , HIS A:252 , LYS A:253binding site for residue SO4 A 302
3AC3SOFTWARECYS A:219 , TYR A:220 , TRP A:232 , VAL A:235 , ASN A:236binding site for residue EMC A 305
4AC4SOFTWAREHIS A:252 , HIS A:256 , LYS A:259 , GLN A:269 , LYS A:273binding site for residue 5KN A 306
5AC5SOFTWAREASN A:167 , ILE A:170 , HIS A:197 , PRO A:199 , ILE A:202binding site for Mono-Saccharide NAG A 303 bound to ASN A 167
6AC6SOFTWARELYS A:181 , ASP A:200 , ASN A:201 , ASN A:272 , THR A:274binding site for Mono-Saccharide NAG A 304 bound to ASN A 272

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5LU8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5LU8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5LU8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5LU8)

(-) Exons   (0, 0)

(no "Exon" information available for 5LU8)

(-) 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:263
                                                                                                                                                                                                                                                                                                       
               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
                 5lu8 A  26 GGKHWVVIVAGSNGWYNYRHQADACHAYQIIHRNGIPDEQIVVMMYDDIAYSEDNPTPGIVINRPNGTDVYQGVPKDYTGEDVTPQNFLAVLRGDAEAVKGIGSGKVLKSGPQDHVFIYFTdHGSTGILVFPNEDLHVKDLNETIHYMYKHKMYRKMVFYIEACESGSMMNHLPDNINVYATTAANPRESSYACYYDEKRSTYLGDWYSVNWMEDSDVEDLTKETLHKQYHLVKSHTQTSHVMQYGNKTISTMKVMQFQGMKR 288
                                    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 C from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 5lu8 C 300 xYVADx 305
                            |    |
                          300-ACE|
                               305-0QE
   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 5LU8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5LU8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5LU8)

(-) Gene Ontology  (21, 21)

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
        LGMN_HUMAN | Q99538: 4aw9 4awa 4awb 4fgu 4n6n 4n6o 5lu9 5lua 5lub

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5LU8)