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(-) Description

Title :  CRYSTAL STRUCTURE OF REDUCED LEGUMAIN IN COMPLEX WITH CYSTATIN E/M
 
Authors :  E. Dall, H. Brandstetter
Date :  14 Oct 13  (Deposition) - 11 Feb 15  (Release) - 11 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Complex, Cysteine Protease, Inhibitor, Legumain, Asparaginyl Endopeptidase, Reactive Center Loop, Papain, Cathepsin, Cancer, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Dall, J. C. Fegg, P. Briza, H. Brandstetter
Structure And Mechanism Of An Aspartimide-Dependent Peptide Ligase In Human Legumain.
Angew. Chem. Int. Ed. Engl. V. 54 2917 2015
PubMed-ID: 25630877  |  Reference-DOI: 10.1002/ANIE.201409135

(-) Compounds

Molecule 1 - LEGUMAIN
    Chains: A
    EC Number: 3.4.22.34
    Engineered: YES
    Expression System: LEISHMANIA TARENTOLAE
    Expression System Taxid: 5689
    Fragment: UNP RESIDUES 26-303
    Gene: LGMN, PRSC1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ASPARAGINYL ENDOPEPTIDASE, PROTEASE, CYSTEINE 1
 
Molecule 2 - CYSTATIN-M
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 29-149
    Gene: CST6
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CYSTATIN-6, CYSTATIN-E

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric/Biological Unit (4, 11)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2IOD5Ligand/IonIODIDE ION
3NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
4SNN1Mod. Amino AcidL-3-AMINOSUCCINIMIDE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:200 , ASN A:201 , ASN A:272 , THR A:274 , NAG A:402 , HOH A:517 , HOH A:524 , HOH A:641BINDING SITE FOR RESIDUE NAG A 401
2AC2SOFTWARENAG A:401 , BMA A:403 , HOH A:508 , HOH A:523 , HOH A:592BINDING SITE FOR RESIDUE NAG A 402
3AC3SOFTWARENAG A:402 , HOH A:508 , HOH A:564 , HOH A:585BINDING SITE FOR RESIDUE BMA A 403
4AC4SOFTWAREHIS A:29 , GLN A:65 , LYS A:287BINDING SITE FOR RESIDUE IOD A 404
5AC5SOFTWAREASN A:196BINDING SITE FOR RESIDUE IOD A 406
6AC6SOFTWARELYS A:164 , ASN A:167 , GLU A:168 , HIS A:171 , HIS A:197 , NAG A:410 , HOH A:606BINDING SITE FOR RESIDUE NAG A 409
7AC7SOFTWARENAG A:409 , HOH A:571BINDING SITE FOR RESIDUE NAG A 410

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1B:101 -B:121

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4N6O)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4N6O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4N6O)

(-) Exons   (0, 0)

(no "Exon" information available for 4N6O)

(-) 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..................................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
                 4n6o 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 B from PDB  Type:PROTEIN  Length:115
                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...hhhhhhhhhhhhhhhhhhh...eeeeeeeeeeeeeee...eeeeeeeeeeeeeee.........hhhhh.........eeeeeeeeeeehhhheeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 4n6o B  11 GELRDLSPDDPQVQKAAQAAVASYNMGSNSIYYFRDTHIIKAQSQLVAGIKYFLTMEMGSTDCRKTRVTGDHVDLTTCPLAAGAQQEKLRCDFEVLVVPWQNSSQLLKHNCVQML 125
                                    20        30        40        50        60        70        80        90       100       110       120
   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 4N6O)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4N6O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4N6O)

(-) Gene Ontology  (29, 30)

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
        CYTM_HUMAN | Q15828: 4n6l 4n6m 4n6n
        LGMN_HUMAN | Q99538: 4aw9 4awa 4awb 4fgu 4n6n 5lu8 5lu9 5lua 5lub

(-) Related Entries Specified in the PDB File

4n6l 4n6m 4n6n