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(-) Description

Title :  CRYSTALLOGRAPHIC ANALYSIS OF A PEPSTATIN ANALOGUE BINDING TO THE ASPARTYL PROTEINASE PENICILLOPEPSIN AT 1.8 ANGSTROMS RESOLUTION
 
Authors :  A. R. Sielecki, M. N. G. James
Date :  16 Dec 91  (Deposition) - 31 Jan 94  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  E,I
Keywords :  Acid Proteinase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. N. G. James, A. R. Sielecki, J. Moult
Crystallographic Analysis Of A Pepstatin Analogue Binding T The Aspartyl Proteinase Penicillopepsin At 1. 8 Angstroms Resolution
Peptides: Structure And V. 1 521 1983 Function, Proceedings Of The Of The Eighth American Peptide Symposium
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PENICILLOPEPSIN
    Chains: E
    EC Number: 3.4.23.20
    Engineered: YES
    Organism Common: PENICILLIUM VITALE
    Organism Scientific: PENICILLIUM JANTHINELLUM
    Organism Taxid: 5079
 
Molecule 2 - INHIBITOR ISOVALERYL (IVA)-VAL-VAL-LYSTA-O-ET (LYSTA IS A LYSYL SIDE CHAIN ANALOGUE OF STATIN
    Chains: I
    Engineered: YES
    Other Details: TRANSITION STATE MIMIC INHIBITOR

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : EI

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1IVA1Mod. Amino AcidISOVALERIC ACID
2LTA1Mod. Amino Acid4,8-DIAMINO-3-HYDROXY-OCTANOIC ACID ETHYL ESTER
3MAN1Ligand/IonALPHA-D-MANNOSE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER E:3 , THR E:9 , PRO E:10 , THR E:11 , GLN E:160 , GLN E:161 , PRO E:162 , HOH E:480 , HOH E:488 , HOH E:503BINDING SITE FOR RESIDUE MAN E 334
2AC2SOFTWAREGLU E:15 , ASP E:33 , GLY E:35 , TYR E:75 , GLY E:76 , ASP E:77 , SER E:79 , PHE E:112 , ILE E:211 , ASP E:213 , GLY E:215 , THR E:216 , THR E:217 , LEU E:218 , HOH I:409 , HOH I:473BINDING SITE FOR CHAIN I OF INHIBITOR ISOVALERYL (IVA)-VAL-VAL-LYSTA-O-ET (LYSTA IS A LYSYL SIDE CHAIN ANALOGUE OF STATIN

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1E:249 -E:283

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gln E:133 -Pro E:134
2Gly E:314 -Pro E:315

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1APT)

(-) PROSITE Motifs  (2, 3)

Asymmetric/Biological Unit (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEPTIDASE_A1PS51767 Peptidase family A1 domain profile.PEPA1_PENJA17-320  1E:17-320
2ASP_PROTEASEPS00141 Eukaryotic and viral aspartyl proteases active site.PEPA1_PENJA30-41
210-221		  2E:30-41
E:210-221

(-) Exons   (0, 0)

(no "Exon" information available for 1APT)

(-) 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 E from PDB  Type:PROTEIN  Length:323
 aligned with PEPA1_PENJA | P00798 from UniProtKB/Swiss-Prot  Length:323

    Alignment length:323
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320   
          PEPA1_PENJA     1 AASGVATNTPTANDEEYITPVTIGGTTLNLNFDTGSADLWVFSTELPASQQSGHSVYNPSATGKELSGYTWSISYGDGSSASGNVFTDSVTVGGVTAHGQAVQAAQQISAQFQQDTNNDGLLGLAFSSINTVQPQSQTTFFDTVKSSLAQPLFAVALKHQQPGVYDFGFIDSSKYTGSLTYTGVDNSQGFWSFNVDSYTAGSQSGDGFSGIADTGTTLLLLDDSVVSQYYSQVSGAQQDSNAGGYVFDCSTNLPDFSVSISGYTATVPGSLINYGPSGDGSTCLGGIQSNSGIGFSIFGDIFLKSQYVVFDSDGPQLGFAPQA 323
               SCOP domains d1apte_ E: Acid protease                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains -----1aptE01 E:6-170 Acid Proteases                                                                                                                                       1aptE02 E:171-322 Acid Proteases                                                                                                                        - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhh...............................hhhhhh.....hhhhhh.............................................hhhhhhh..........hhhhh........hhhhhhh.........................hhhh.................eeeeeeeee..eeeeeeeeee......eeehhhhhhhhhh.....eee....eeee........eeeee..eeeeehhhhheeee......eee.eee......eeehhhhhh................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------PEPTIDASE_A1  PDB: E:17-320 UniProt: 17-320                                                                                                                                                                                                                                                                     --- PROSITE (1)
                PROSITE (2) -----------------------------ASP_PROTEASE------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASP_PROTEASE------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1apt E   1 AASGVATNTPTANDEEYITPVTIGGTTLNLNFDTGSADLWVFSTELPASQQSGHSVYNPSATGKELSGYTWSISYGDGSSASGNVFTDSVTVGGVTAHGQAVQAAQQISAQFQQDTNNDGLLGLAFSSINTVQPQSQTTFFDTVKSSLAQPLFAVALKHQQPGVYDFGFIDSSKYTGSLTYTGVDNSQGFWSFNVDSYTAGSQSGDGFSGIADTGTTLLLLDDSVVSQYYSQVSGAQQDSNAGGYVFDCSTNLPDFSVSISGYTATVPGSLINYGPSGDGSTCLGGIQSNSGIGFSIFGDIFLKSQYVVFDSDGPQLGFAPQA 323
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320   


Chain I from PDB  Type:PROTEIN  Length:4
                                    
               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
                 1apt I   4 xVVx   1
                            ||||
                            4-IVA
                             3||
                              2|
                               1-LTA
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1APT)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain E   (PEPA1_PENJA | P00798)
molecular function
    GO:0004190    aspartic-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PEPA1_PENJA | P00798: 1apu 1apv 1apw 1bxo 1bxq 1ppk 1ppl 1ppm 2wea 2web 2wec 2wed 3app

(-) Related Entries Specified in the PDB File

1apu 1apv 1apw