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(-) Description

Title :  ACID PROTEINASE (PENICILLOPEPSIN) COMPLEX WITH PHOSPHONATE INHIBITOR.
 
Authors :  J. C. Parrish, A. R. Khan, M. E. Fraser, W. W. Smith, P. A. Bartlett, M. N. G
Date :  07 Oct 98  (Deposition) - 14 Oct 98  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.41
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Phosphonate Inhibitors (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. R. Khan, J. C. Parrish, M. E. Fraser, W. W. Smith, P. A. Bartlett, M. N. James
Lowering The Entropic Barrier For Binding Conformationally Flexible Inhibitors To Enzymes.
Biochemistry V. 37 16839 1998
PubMed-ID: 9836576  |  Reference-DOI: 10.1021/BI9821364
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (PENICILLOPEPSIN)
    Chains: A
    EC Number: 3.4.23.20
    Organism Scientific: PENICILLIUM JANTHINELLUM
    Organism Taxid: 5079

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 9)

Asymmetric/Biological Unit (5, 9)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL3Ligand/IonGLYCEROL
3MAN2Ligand/IonALPHA-D-MANNOSE
4PP81Ligand/Ion2-[(1R)-1-(N-(3-METHYLBUTANOYL)-L-VALYL-L-ASPARAGINYL)-AMINO)-3-METHYLBUTYL]HYDROXYPHOSPHINYLOXY]-3-PHENYLPROPANOIC ACID METHYLESTER
5SO42Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:3 , THR A:9 , PRO A:10 , THR A:11 , GLN A:160 , GLN A:161 , PRO A:162 , HOH A:404 , HOH A:452 , HOH A:636BINDING SITE FOR RESIDUE MAN A 331
02AC2SOFTWARETHR A:7 , GLN A:150 , HOH A:573 , HOH A:734BINDING SITE FOR RESIDUE MAN A 332
03AC3SOFTWARETYR A:175 , SER A:178 , LEU A:179 , HOH A:522 , HOH A:542 , HOH A:747 , HOH A:793BINDING SITE FOR RESIDUE SO4 A 325
04AC4SOFTWARESER A:109 , ALA A:110 , HOH A:476 , HOH A:494BINDING SITE FOR RESIDUE SO4 A 326
05AC5SOFTWAREGLY A:68 , GLY A:76 , ILE A:293 , PP8 A:324 , HOH A:432 , HOH A:732 , HOH A:799BINDING SITE FOR RESIDUE ACT A 330
06AC6SOFTWAREGLU A:15 , ASP A:33 , GLY A:35 , TYR A:75 , GLY A:76 , ASP A:77 , SER A:79 , GLN A:111 , GLN A:133 , PRO A:134 , ASP A:213 , GLY A:215 , THR A:216 , THR A:217 , ILE A:297 , ACT A:330 , HOH A:411 , HOH A:568 , HOH A:610 , HOH A:732BINDING SITE FOR RESIDUE PP8 A 324
07AC7SOFTWAREPRO A:20 , THR A:22 , THR A:91 , GLY A:93 , GLY A:94 , SER A:172 , HOH A:465 , HOH A:522 , HOH A:572BINDING SITE FOR RESIDUE GOL A 327
08AC8SOFTWAREGLN A:135 , GLN A:188 , SER A:192 , SER A:209 , GLN A:238 , PHE A:295 , HOH A:528 , HOH A:539 , HOH A:800BINDING SITE FOR RESIDUE GOL A 328
09AC9SOFTWAREGLU A:65 , ASN A:84 , SER A:197 , TYR A:198 , THR A:199 , SER A:259 , HOH A:506 , HOH A:540 , HOH A:559BINDING SITE FOR RESIDUE GOL A 329
10CICAUTHORASP A:33 , ASP A:213CATALYTIC RESIDUES

(-) SS Bonds  (1, 1)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological 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 1BXQ)

(-) PROSITE Motifs  (2, 3)

Asymmetric/Biological 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

(-) Exons   (0, 0)

(no "Exon" information available for 1BXQ)

(-) 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: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 d1bxqa_ A: Acid protease                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains -----1bxqA01 A:6-170 Acid Proteases                                                                                                                                       1bxqA02 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.hhhh......eeee...hhh..........hhhhhhhh....eeeee......eeeee....hhh.....eeee........eeee.eeee..eeee.eeeee......eee.hhhhhhhhhh....eee....eee.........eeeee..eeeee.hhhheeee......eee.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
                 1bxq 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)
  - → 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 1BXQ)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological 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 | P00798: 1apt 1apu 1apv 1apw 1bxo 1ppk 1ppl 1ppm 2wea 2web 2wec 2wed 3app

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1BXQ)