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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PORCINE CARBOXYPEPTIDASE B - ANABAENOPEPTIN F COMPLEX
 
Authors :  H. Schreuder, A. Liesum, P. Loenze
Date :  19 Aug 16  (Deposition) - 21 Sep 16  (Release) - 21 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,F,G,H
Biol. Unit 1:  A,F  (1x)
Biol. Unit 2:  B,G  (1x)
Biol. Unit 3:  C,H  (1x)
Keywords :  Drug Discovery, Natural Compound, Tafi Inhibitor, Anabaenopeptin, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Schreuder, A. Liesum, P. Lonze, H. Stump, H. Hoffmann, M. Schiell, M. Kurz, L. Toti, A. Bauer, C. Kallus, C. Klemke-Jahn, J. Czech, D. Kramer, H. Enke, T. H. Niedermeyer, V. Morrison, V. Kumar, M. Bronstrup
Isolation, Co-Crystallization And Structure-Based Characterization Of Anabaenopeptins As Highly Potent Inhibitors Of Activated Thrombin Activatable Fibrinolysis Inhibitor (Tafia).
Sci Rep V. 6 32958 2016
PubMed-ID: 27604544  |  Reference-DOI: 10.1038/SREP32958

(-) Compounds

Molecule 1 - CARBOXYPEPTIDASE B
    Chains: A, B, C
    EC Number: 3.4.17.2
    Fragment: UNP RESIDUES 111-416
    Organism Common: PIG
    Organism Scientific: SUS SCROFA
    Organism Taxid: 9823
 
Molecule 2 - ANABAENOPEPTIN F
    Chains: F, G, H
    Organism Scientific: PLANKTOTHRIX RUBESCENS
    Organism Taxid: 59512
    Strain: CBT287

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCFGH
Biological Unit 1 (1x): A  F  
Biological Unit 2 (1x):  B  G 
Biological Unit 3 (1x):   C  H

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 18)

Asymmetric Unit (6, 18)
No.NameCountTypeFull Name
173N3Mod. Amino Acid(2~{S})-5-CARBAMIMIDAMIDO-2-(CARBOXYAMINO)PENTANOICACID
273O3Mod. Amino Acid(2~{S})-2-AZANYL-4-(4-HYDROXYPHENYL)BUTANOIC ACID
3DLY3Mod. Amino AcidD-LYSINE
4IIL3Mod. Amino AcidISO-ISOLEUCINE
5MAA3Mod. Amino AcidN-METHYL-L-ALANINE
6ZN3Ligand/IonZINC ION
Biological Unit 1 (5, 5)
No.NameCountTypeFull Name
173N1Mod. Amino Acid(2~{S})-5-CARBAMIMIDAMIDO-2-(CARBOXYAMINO)PENTANOICACID
273O1Mod. Amino Acid(2~{S})-2-AZANYL-4-(4-HYDROXYPHENYL)BUTANOIC ACID
3DLY1Mod. Amino AcidD-LYSINE
4IIL1Mod. Amino AcidISO-ISOLEUCINE
5MAA1Mod. Amino AcidN-METHYL-L-ALANINE
6ZN-1Ligand/IonZINC ION
Biological Unit 2 (5, 5)
No.NameCountTypeFull Name
173N1Mod. Amino Acid(2~{S})-5-CARBAMIMIDAMIDO-2-(CARBOXYAMINO)PENTANOICACID
273O1Mod. Amino Acid(2~{S})-2-AZANYL-4-(4-HYDROXYPHENYL)BUTANOIC ACID
3DLY1Mod. Amino AcidD-LYSINE
4IIL1Mod. Amino AcidISO-ISOLEUCINE
5MAA1Mod. Amino AcidN-METHYL-L-ALANINE
6ZN-1Ligand/IonZINC ION
Biological Unit 3 (5, 5)
No.NameCountTypeFull Name
173N1Mod. Amino Acid(2~{S})-5-CARBAMIMIDAMIDO-2-(CARBOXYAMINO)PENTANOICACID
273O1Mod. Amino Acid(2~{S})-2-AZANYL-4-(4-HYDROXYPHENYL)BUTANOIC ACID
3DLY1Mod. Amino AcidD-LYSINE
4IIL1Mod. Amino AcidISO-ISOLEUCINE
5MAA1Mod. Amino AcidN-METHYL-L-ALANINE
6ZN-1Ligand/IonZINC ION

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:69 , GLU A:72 , HIS A:196 , 73N F:1binding site for residue ZN A 401
02AC2SOFTWAREHIS B:69 , GLU B:72 , HIS B:196 , HOH B:529 , 73N G:1binding site for residue ZN B 401
03AC3SOFTWAREHIS C:69 , GLU C:72 , HIS C:196 , HOH C:552 , 73N H:1binding site for residue ZN C 401
04AC4SOFTWAREHIS A:69 , ARG A:71 , ARG A:127 , ASN A:144 , ARG A:145 , TYR A:198 , SER A:207 , TYR A:248 , ALA A:250 , GLY A:253 , ASP A:255 , THR A:268 , GLU A:270 , PHE A:279 , ZN A:401 , HOH A:552 , HOH A:598 , HOH A:604 , IIL F:3 , 73O F:4 , MAA F:5 , PHE F:6 , HOH F:102binding site for Di-peptide 73N F 1 and DLY F 2
05AC5SOFTWAREARG A:71 , ARG A:127 , ARG A:145 , GLU A:163 , THR A:164 , TYR A:198 , TYR A:248 , PHE A:279 , HOH A:552 , 73N F:1 , 73O F:4 , MAA F:5 , PHE F:6 , HOH F:102binding site for Di-peptide DLY F 2 and IIL F 3
06AC6SOFTWAREARG A:71 , ARG A:127 , TYR A:198 , TYR A:248 , PHE A:279 , HOH A:552 , 73N F:1 , IIL F:3 , 73O F:4 , MAA F:5 , HOH F:102binding site for Di-peptide DLY F 2 and PHE F 6
07AC7SOFTWAREARG A:71 , MET A:125 , ARG A:127 , ARG A:145 , GLU A:163 , THR A:164 , TYR A:248 , 73N F:1 , DLY F:2 , MAA F:5 , PHE F:6 , HOH F:101binding site for residues IIL F 3 and 73O F 4
08AC8SOFTWAREARG A:71 , MET A:125 , GLU A:163 , DLY F:2 , IIL F:3 , PHE F:6 , HOH F:101binding site for residues 73O F 4 and MAA F 5
09AC9SOFTWAREDLY F:2 , IIL F:3 , 73O F:4binding site for Di-peptide MAA F 5 and PHE F 6
10AD1SOFTWAREHIS B:69 , ARG B:71 , ARG B:127 , ASN B:144 , ARG B:145 , TYR B:198 , SER B:207 , TYR B:248 , ALA B:250 , GLY B:253 , ASP B:255 , GLU B:270 , PHE B:279 , ZN B:401 , HOH B:514 , HOH B:529 , HOH B:558 , HOH B:596 , HOH B:640 , HOH B:650 , HOH B:704 , IIL G:3 , 73O G:4 , MAA G:5 , PHE G:6binding site for Di-peptide 73N G 1 and DLY G 2
11AD2SOFTWAREARG B:71 , ARG B:127 , ARG B:145 , GLU B:163 , TYR B:198 , TYR B:248 , PHE B:279 , HOH B:514 , HOH B:529 , HOH B:596 , HOH B:704 , 73N G:1 , 73O G:4 , MAA G:5 , PHE G:6binding site for Di-peptide DLY G 2 and IIL G 3
12AD3SOFTWAREARG B:71 , ARG B:127 , TYR B:198 , TYR B:248 , PHE B:279 , HOH B:514 , HOH B:529 , HOH B:596 , HOH B:704 , LEU C:308 , 73N G:1 , IIL G:3 , 73O G:4 , MAA G:5 , HOH G:103binding site for Di-peptide DLY G 2 and PHE G 6
13AD4SOFTWAREGLU B:16 , ARG B:71 , MET B:125 , ARG B:127 , ARG B:145 , GLU B:163 , TYR B:248 , HOH B:554 , HOH B:620 , 73N G:1 , DLY G:2 , MAA G:5 , PHE G:6 , HOH G:101binding site for residues IIL G 3 and 73O G 4
14AD5SOFTWAREGLU B:16 , ARG B:71 , MET B:125 , GLU B:163 , HOH B:554 , HOH B:620 , DLY G:2 , IIL G:3 , PHE G:6 , HOH G:101 , HOH G:102binding site for residues 73O G 4 and MAA G 5
15AD6SOFTWARELEU C:308 , DLY G:2 , IIL G:3 , 73O G:4 , HOH G:102 , HOH G:103binding site for Di-peptide MAA G 5 and PHE G 6
16AD7SOFTWAREHIS C:69 , ARG C:71 , ARG C:127 , ASN C:144 , ARG C:145 , TYR C:198 , SER C:207 , TYR C:248 , ALA C:250 , GLY C:253 , ASP C:255 , GLU C:270 , PHE C:279 , ZN C:401 , HOH C:552 , HOH C:574 , IIL H:3 , 73O H:4 , MAA H:5 , PHE H:6 , HOH H:103binding site for Di-peptide 73N H 1 and DLY H 2
17AD8SOFTWAREARG C:71 , ARG C:127 , TYR C:198 , TYR C:248 , PHE C:279 , HOH C:552 , 73N H:1 , IIL H:3 , 73O H:4 , MAA H:5 , HOH H:102 , HOH H:103binding site for Di-peptide DLY H 2 and PHE H 6
18AD9SOFTWAREARG C:71 , ARG C:127 , ARG C:145 , GLU C:163 , THR C:164 , TYR C:198 , TYR C:248 , PHE C:279 , HOH C:552 , 73N H:1 , 73O H:4 , MAA H:5 , PHE H:6 , HOH H:103binding site for Di-peptide DLY H 2 and IIL H 3
19AE1SOFTWARETRP C:15 , GLU C:16 , ARG C:71 , MET C:125 , ARG C:127 , ARG C:145 , GLU C:163 , THR C:164 , TYR C:248 , 73N H:1 , DLY H:2 , MAA H:5 , PHE H:6 , HOH H:101binding site for residues IIL H 3 and 73O H 4
20AE2SOFTWARETRP C:15 , GLU C:16 , ARG C:71 , MET C:125 , GLU C:163 , HOH C:770 , DLY H:2 , IIL H:3 , PHE H:6 , HOH H:101binding site for residues 73O H 4 and MAA H 5
21AE3SOFTWAREHOH C:770 , DLY H:2 , IIL H:3 , 73O H:4 , HOH H:102binding site for Di-peptide MAA H 5 and PHE H 6

(-) SS Bonds  (9, 9)

Asymmetric Unit
No.Residues
1A:66 -A:79
2A:138 -A:161
3A:152 -A:166
4B:66 -B:79
5B:138 -B:161
6B:152 -B:166
7C:66 -C:79
8C:138 -C:161
9C:152 -C:166

(-) Cis Peptide Bonds  (9, 9)

Asymmetric Unit
No.Residues
1Ser A:197 -Tyr A:198
2Pro A:205 -Tyr A:206
3Arg A:272 -Asp A:273
4Ser B:197 -Tyr B:198
5Pro B:205 -Tyr B:206
6Arg B:272 -Asp B:273
7Ser C:197 -Tyr C:198
8Pro C:205 -Tyr C:206
9Arg C:272 -Asp C:273

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5LRK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5LRK)

(-) Exons   (0, 0)

(no "Exon" information available for 5LRK)

(-) 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:304
                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhh...eeeeeeee.....eeeeeee........eeeee......hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhheeeee...hhhhhhhhhhh...................hhhhh..........................hhhhhhhhhhhhh....eeeeeeee....eeee..........hhhhhhhhhhhhhhhhhh......eeeehhhhh.....hhhhhhhhh...eeeeee...........hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5lrk A    6 GHSYEKYNNWETIEAWTKQVTSENPDLISRTAIGTTFLGNNIYLLKVGKPGPNKPAIFMDCGFHAREWISHAFCQWFVREAVLTYGYESHMTEFLNKLDFYVLPVLNIDGYIYTWTKNRMWRKTRSTNAGTTCIGTDPNRNFDAGWCTTGASTDPCDETYCGSAAESEKETKALADFIRNNLSSIKAYLTIHSYSQMILYPYSYDYKLPENNAELNNLAKAAVKELATLYGTKYTYGPGATTIYPAAGGSDDWAYDQGIKYSFTFELRDKGRYGFILPESQIQATCEETMLAIKYVTNYVLGHL  308
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185   |   194       204       214       224       234       244       254       264       274       284       294       304    
                                                                                                                                                                                                                188A                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:304
                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhh...eeeeeeee.....eeeeeee........eeeeee.....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhheeeee...hhhhhhhhhhh...................hhhhh..........................hhhhhhhhhhhhhh...eeeeeeee....eeee..........hhhhhhhhhhhhhhhhhhhhh...eeeehhhhh.....hhhhhhhhh...eeeeee...........hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5lrk B    6 GHSYEKYNNWETIEAWTKQVTSENPDLISRTAIGTTFLGNNIYLLKVGKPGPNKPAIFMDCGFHAREWISHAFCQWFVREAVLTYGYESHMTEFLNKLDFYVLPVLNIDGYIYTWTKNRMWRKTRSTNAGTTCIGTDPNRNFDAGWCTTGASTDPCDETYCGSAAESEKETKALADFIRNNLSSIKAYLTIHSYSQMILYPYSYDYKLPENNAELNNLAKAAVKELATLYGTKYTYGPGATTIYPAAGGSDDWAYDQGIKYSFTFELRDKGRYGFILPESQIQATCEETMLAIKYVTNYVLGHL  308
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185   |   194       204       214       224       234       244       254       264       274       284       294       304    
                                                                                                                                                                                                                188A                                                                                                                        


Chain C from PDB  Type:PROTEIN  Length:304
                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhh....eeeeeeee.....eeeeeee........eeeeee.....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhheeeee...hhhhhhhhhhh...................hhhhh..........................hhhhhhhhhhhhh....eeeeeeee....eeee..........hhhhhhhhhhhhhhhhhh......eeeehhhhh.....hhhhhhhhh...eeeeee...........hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5lrk C    6 GHSYEKYNNWETIEAWTKQVTSENPDLISRTAIGTTFLGNNIYLLKVGKPGPNKPAIFMDCGFHAREWISHAFCQWFVREAVLTYGYESHMTEFLNKLDFYVLPVLNIDGYIYTWTKNRMWRKTRSTNAGTTCIGTDPNRNFDAGWCTTGASTDPCDETYCGSAAESEKETKALADFIRNNLSSIKAYLTIHSYSQMILYPYSYDYKLPENNAELNNLAKAAVKELATLYGTKYTYGPGATTIYPAAGGSDDWAYDQGIKYSFTFELRDKGRYGFILPESQIQATCEETMLAIKYVTNYVLGHL  308
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185   |   194       204       214       224       234       244       254       264       274       284       294       304    
                                                                                                                                                                                                                188A                                                                                                                        


Chain F from PDB  Type:PROTEIN  Length:6
                                       
               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
                5lrk F    1 xxxxxF    6
                            ||||| 
                            1-73N 
                             2-DLY
                              3-IIL
                               4-73O
                                5-MAA


Chain G from PDB  Type:PROTEIN  Length:6
                                       
               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
                5lrk G    1 xxxxxF    6
                            ||||| 
                            ||||| 
                            1-73N 
                             2-DLY
                              3-IIL
                               4-73O
                                5-MAA


Chain H from PDB  Type:PROTEIN  Length:6
                                       
               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
                5lrk H    1 xxxxxF    6
                            ||||| 
                            ||||| 
                            1-73N 
                             2-DLY
                              3-IIL
                               4-73O
                                5-MAA
   Legend:   → Mismatch (orange background)
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  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 5LRK)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5LRK)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5LRK)

(-) Gene Ontology  (10, 10)

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    Protein Cavities: castP
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    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  CBPB1_PIG | P09955
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        CBPB1_PIG | P09955: 1nsa 1pba 1z5r 1zg7 1zg8 1zg9 2jew 2piy 2piz 2pj0 2pj1 2pj2 2pj3 2pj4 2pj5 2pj6 2pj7 2pj8 2pj9 2pja 2pjb 2pjc 3glj 3wab 3wc5 3wc6 3wc7 4uia 4uib 4z65 5j1q 5jc6 5lrg 5lrj 5lyd 5lyf 5lyi 5lyl

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5LRK)