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(-) Description

Title :  CRYSTAL STRUCTURE OF OXIDIZED LEGUMAIN IN COMPLEX WITH CYSTATIN E/M
 
Authors :  E. Dall, H. Brandstetter
Date :  14 Oct 13  (Deposition) - 18 Feb 15  (Release) - 11 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.87
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 Strain: P10
    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  (5, 12)

Asymmetric/Biological Unit (5, 12)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2IOD5Ligand/IonIODIDE ION
3NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
4SCH1Mod. Amino AcidS-METHYL-THIO-CYSTEINE
5SNN1Mod. Amino AcidL-3-AMINOSUCCINIMIDE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:65 , LYS A:287BINDING SITE FOR RESIDUE IOD A 401
2AC2SOFTWAREASN A:196BINDING SITE FOR RESIDUE IOD A 403
3AC3SOFTWARELYS A:181 , ASP A:200 , ASN A:201 , ASN A:272 , THR A:274 , NAG A:407 , HOH A:532BINDING SITE FOR RESIDUE NAG A 406
4AC4SOFTWARENAG A:406 , BMA A:408BINDING SITE FOR RESIDUE NAG A 407
5AC5SOFTWARENAG A:407BINDING SITE FOR RESIDUE BMA A 408
6AC6SOFTWAREASN A:167 , HIS A:171 , HIS A:197 , NAG A:410 , HOH A:599BINDING SITE FOR RESIDUE NAG A 409
7AC7SOFTWARENAG A:409BINDING SITE FOR RESIDUE NAG A 410

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1B:88 -B:73
2B:121 -B:101

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4N6N)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4N6N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4N6N)

(-) Exons   (0, 0)

(no "Exon" information available for 4N6N)

(-) 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....eeeeehhhhhhhhhhh.......hhhhhhhhhhhhh.....eeee.hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4n6n 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                                   189-SCH                                                                                               


Chain B from PDB  Type:PROTEIN  Length:117
                                                                                                                                                     
               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
                 4n6n B  10 VGELRDLSPDDPQVQKAAQAAVASYNMGSNSIYYFRDTHIIKAQSQLVAGIKYFLTMEMGSTDCRKTRVTGDHVDLTTCPLAAGAQQEKLRCDFEVLVVPWQNSSQLLKHNCVQMLE 126
                                    19        29        39        49        59        69        79        89        99       109       119
   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 4N6N)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4N6N)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4N6N)

(-) Gene Ontology  (29, 30)

Asymmetric/Biological Unit(hide GO term definitions)

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  LGMN_HUMAN | Q99538
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 Related Entries

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

UniProtKB/Swiss-Prot
        CYTM_HUMAN | Q15828: 4n6l 4n6m 4n6o
        LGMN_HUMAN | Q99538: 4aw9 4awa 4awb 4fgu 4n6o 5lu8 5lu9 5lua 5lub

(-) Related Entries Specified in the PDB File

4n6l 4n6m 4n6o