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(-) Description

Title :  ACID PROTEINASE (PENICILLOPEPSIN) (E.C.3.4.23.20) COMPLEX WITH PHOSPHONATE INHIBITOR: METHYL(2S)-[1-(((N-FORMYL)-L-VALYL)AMINO-2-(2-NAPHTHYL)ETHYL)HYDROXYPHOSPHINYLOXY]-3-PHENYLPROPANOATE, SODIUM SALT
 
Authors :  J. Ding, M. E. Fraser, M. N. G. James
Date :  03 Feb 98  (Deposition) - 27 May 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Penicillopepsin, Phosphonate Inhibitor, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Ding, M. E. Fraser, J. H. Meyer, P. A. Bartlett, M. N. G. James
Macrocyclic Inhibitors Of Penicillopepsin. Ii. X-Ray Crystallographic Analyses Of Penicillopepsin Complexed With A P3-P1 Macrocyclic Peptidyl Inhibitor And With Its Two Acyclic Analogues
J. Am. Chem. Soc. V. 120 4610 1998
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PENICILLOPEPSIN
    ChainsA
    EC Number3.4.23.20
    Organism ScientificPENICILLIUM JANTHINELLUM
    Organism Taxid5079

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1MAN2Ligand/IonALPHA-D-MANNOSE
2PP41Ligand/IonMETHYL (2S)-[1-((N-FORMYL)-L-VALYL)AMINO-2-(2-NAPHTHYL)ETHYL)HYDROXYPHOSPHINYLOXY]-3-PHENYLPROPANOATE
3SO41Ligand/IonSULFATE ION
Biological Unit 1 (3, 8)
No.NameCountTypeFull Name
1MAN4Ligand/IonALPHA-D-MANNOSE
2PP42Ligand/IonMETHYL (2S)-[1-((N-FORMYL)-L-VALYL)AMINO-2-(2-NAPHTHYL)ETHYL)HYDROXYPHOSPHINYLOXY]-3-PHENYLPROPANOATE
3SO42Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:3 , THR A:9 , PRO A:10 , THR A:11 , ALA A:12 , GLN A:160 , GLN A:161 , PRO A:162 , HOH A:382 , HOH A:516 , HOH A:550 , HOH A:587BINDING SITE FOR RESIDUE MAN A 324
2AC2SOFTWARETHR A:7 , HOH A:614BINDING SITE FOR RESIDUE MAN A 325
3AC3SOFTWARETYR A:175 , SER A:178 , LEU A:179 , HOH A:506 , HOH A:594BINDING SITE FOR RESIDUE SO4 A 329
4AC4SOFTWAREASN A:31 , ASP A:33 , GLY A:35 , TYR A:75 , GLY A:76 , ASP A:77 , SER A:79 , PHE A:112 , ASP A:115 , GLN A:133 , ASP A:213 , GLY A:215 , THR A:216 , THR A:217 , HOH A:386 , HOH A:562BINDING SITE FOR RESIDUE PP4 A 326
5CICUNKNOWNASP A:33 , ASP A:213CATALYTIC SITE.

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:249 -A:283

(-) Cis Peptide Bonds  (2, 2)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WEB)

(-) PROSITE Motifs  (2, 3)

Asymmetric Unit (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEPTIDASE_A1PS51767 Peptidase family A1 domain profile.PEPA1_PENJA17-320  1A:17-320
2ASP_PROTEASEPS00141 Eukaryotic and viral aspartyl proteases active site.PEPA1_PENJA30-41
210-221
  2A:30-41
A:210-221
Biological Unit 1 (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEPTIDASE_A1PS51767 Peptidase family A1 domain profile.PEPA1_PENJA17-320  2A:17-320
2ASP_PROTEASEPS00141 Eukaryotic and viral aspartyl proteases active site.PEPA1_PENJA30-41
210-221
  4A:30-41
A:210-221

(-) Exons   (0, 0)

(no "Exon" information available for 2WEB)

(-) 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: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 d2weba_ A: Acid protease                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains -----2webA01 A:6-170 Acid Proteases                                                                                                                                       2webA02 A:171-322 Acid Proteases                                                                                                                        - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.hhh..eeeeeee..eeeeeeee.....eee......hhhh.......hhhh.......eeeee.....eeeeeeeee.eee..eee..eeeeeeeee.hhhhh.....eeee...hhh..........hhhhhhhh....eeeee......eeeee....hhh.....eeee........eeee.eeee..eeee.eeeee......eee.hhhhhhhhhh....eee....eeeee.......eeeee..eeeee.hhhheeee.....eeee.eee......eee.hhhhhheeeeee....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------PEPTIDASE_A1  PDB: A:17-320 UniProt: 17-320                                                                                                                                                                                                                                                                     --- PROSITE (1)
                PROSITE (2) -----------------------------ASP_PROTEASE------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASP_PROTEASE------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2web A   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   

   Legend:   → Mismatch (orange background)
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  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 Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2WEB)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (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 | P007981apt 1apu 1apv 1apw 1bxo 1bxq 1ppk 1ppl 1ppm 2wea 2wec 2wed 3app

(-) Related Entries Specified in the PDB File

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