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(-) Description

Title :  R39-IMIPENEM ACYL-ENZYME CRYSTAL STRUCTURE
 
Authors :  D. Van Elder, E. Sauvage, R. Herman, F. Kerff, M. Rocaboy, P. Charlier
Date :  11 Mar 13  (Deposition) - 20 Mar 13  (Release) - 20 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Hydrolase, Penicillin-Binding, Acyl-Enzyme (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Sauvage, D. Van Elder, R. Herman, F. Kerff, R. F. Pratt, P. Charlier
Crystal Structures Of R39-Imipenem Acyl-Enzyme.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - D-ALANYL-D-ALANINE CARBOXYPEPTIDASE
    Chains: A, B, C, D
    EC Number: 3.4.16.4
    Organism Scientific: ACTINOMADURA SP. R39
    Organism Taxid: 72570
    Synonym: DD-CARBOXYPEPTIDASE, DD-PEPTIDASE, PENICILLIN-BINDING PROTEIN, PBP

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 44)

Asymmetric Unit (5, 44)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2IM24Ligand/Ion(5R)-5-[(1S,2R)-1-FORMYL-2-HYDROXYPROPYL]-3-[(2-{[(E)-IMINOMETHYL]AMINO}ETHYL)SULFANYL]-4,5-DIHYDRO-1H-PYRROLE-2-CARBOXYLIC ACID
3MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4MG4Ligand/IonMAGNESIUM ION
5SO433Ligand/IonSULFATE ION
Biological Unit 1 (3, 13)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2IM21Ligand/Ion(5R)-5-[(1S,2R)-1-FORMYL-2-HYDROXYPROPYL]-3-[(2-{[(E)-IMINOMETHYL]AMINO}ETHYL)SULFANYL]-4,5-DIHYDRO-1H-PYRROLE-2-CARBOXYLIC ACID
3MES-1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4MG-1Ligand/IonMAGNESIUM ION
5SO411Ligand/IonSULFATE ION
Biological Unit 2 (2, 9)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2IM21Ligand/Ion(5R)-5-[(1S,2R)-1-FORMYL-2-HYDROXYPROPYL]-3-[(2-{[(E)-IMINOMETHYL]AMINO}ETHYL)SULFANYL]-4,5-DIHYDRO-1H-PYRROLE-2-CARBOXYLIC ACID
3MES-1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4MG-1Ligand/IonMAGNESIUM ION
5SO48Ligand/IonSULFATE ION
Biological Unit 3 (2, 8)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2IM21Ligand/Ion(5R)-5-[(1S,2R)-1-FORMYL-2-HYDROXYPROPYL]-3-[(2-{[(E)-IMINOMETHYL]AMINO}ETHYL)SULFANYL]-4,5-DIHYDRO-1H-PYRROLE-2-CARBOXYLIC ACID
3MES-1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4MG-1Ligand/IonMAGNESIUM ION
5SO47Ligand/IonSULFATE ION
Biological Unit 4 (4, 10)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2IM21Ligand/Ion(5R)-5-[(1S,2R)-1-FORMYL-2-HYDROXYPROPYL]-3-[(2-{[(E)-IMINOMETHYL]AMINO}ETHYL)SULFANYL]-4,5-DIHYDRO-1H-PYRROLE-2-CARBOXYLIC ACID
3MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4MG-1Ligand/IonMAGNESIUM ION
5SO47Ligand/IonSULFATE ION

(-) Sites  (44, 44)

Asymmetric Unit (44, 44)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:282 , THR A:283 , HOH A:2076 , HOH A:2077 , HOH A:2177 , HOH A:2180BINDING SITE FOR RESIDUE SO4 A1467
02AC2SOFTWAREALA A:234 , ARG A:236 , HOH A:2166BINDING SITE FOR RESIDUE SO4 A1468
03AC3SOFTWARESER A:131 , ARG A:133 , LEU A:134BINDING SITE FOR RESIDUE SO4 A1469
04AC4SOFTWAREGLY A:159 , GLU A:160 , ARG A:161 , SO4 A:1476 , HOH A:2123 , HOH A:2129BINDING SITE FOR RESIDUE SO4 A1470
05AC5SOFTWAREGLU A:188 , HIS A:247 , GLU A:251BINDING SITE FOR RESIDUE MG A 610
06AC6SOFTWAREALA A:402 , VAL A:406 , HIS A:462 , GLN A:463 , HOH A:2228BINDING SITE FOR RESIDUE MG A 611
07AC7SOFTWAREGLY A:268 , HOH A:2056BINDING SITE FOR RESIDUE GOL A1471
08AC8SOFTWAREASP B:281 , HIS B:282 , THR B:283 , HOH B:2066BINDING SITE FOR RESIDUE SO4 B1466
09AC9SOFTWAREALA B:234 , ARG B:236 , HOH B:2157 , HOH B:2220 , HOH B:2221BINDING SITE FOR RESIDUE SO4 B1467
10BC1SOFTWARESER B:131 , ARG B:133 , LEU B:134BINDING SITE FOR RESIDUE SO4 B1468
11BC2SOFTWARESO4 A:1475 , GLY B:159 , GLU B:160 , ARG B:161 , SO4 B:1472BINDING SITE FOR RESIDUE SO4 B1469
12BC3SOFTWAREHIS C:282 , THR C:283 , HOH C:2069 , HOH C:2070BINDING SITE FOR RESIDUE SO4 C1466
13BC4SOFTWAREALA C:234 , ARG C:236 , HOH C:2166 , HOH C:2235BINDING SITE FOR RESIDUE SO4 C1467
14BC5SOFTWARESER C:131 , GLU C:132 , ARG C:133 , LEU C:134 , HOH C:2236BINDING SITE FOR RESIDUE SO4 C1468
15BC6SOFTWAREGLY C:159 , GLU C:160 , ARG C:161 , SO4 C:1472 , HOH C:2117BINDING SITE FOR RESIDUE SO4 C1469
16BC7SOFTWAREHIS D:282 , THR D:283 , HOH D:2083 , HOH D:2084 , HOH D:2200BINDING SITE FOR RESIDUE SO4 D1467
17BC8SOFTWAREARG D:236 , HOH D:2187BINDING SITE FOR RESIDUE SO4 D1468
18BC9SOFTWARESER D:131 , ARG D:133 , LEU D:134 , HOH D:2267BINDING SITE FOR RESIDUE SO4 D1469
19CC1SOFTWAREGLY D:159 , GLU D:160 , ARG D:161 , SO4 D:1474 , HOH D:2139BINDING SITE FOR RESIDUE SO4 D1470
20CC2SOFTWAREGLU D:188 , HIS D:247 , GLU D:251BINDING SITE FOR RESIDUE MG D 610
21CC3SOFTWAREVAL D:406 , HIS D:462BINDING SITE FOR RESIDUE MG D 611
22CC4SOFTWAREGLY D:268BINDING SITE FOR RESIDUE GOL D1471
23CC5SOFTWAREHIS C:158 , GLY C:159 , SO4 C:1472BINDING SITE FOR RESIDUE SO4 C1470
24CC6SOFTWAREASN D:195 , HOH D:2161 , HOH D:2166BINDING SITE FOR RESIDUE SO4 D1472
25CC7SOFTWARESER B:38 , ARG B:39 , ASP B:40 , HOH B:2018BINDING SITE FOR RESIDUE SO4 B1470
26CC8SOFTWAREASP A:130 , SER A:131BINDING SITE FOR RESIDUE SO4 A1472
27CC9SOFTWAREGLY A:70 , ARG A:93 , HOH A:2040BINDING SITE FOR RESIDUE SO4 A1473
28DC1SOFTWAREGLY D:70 , ARG D:93 , HOH D:2045BINDING SITE FOR RESIDUE SO4 D1473
29DC2SOFTWAREARG A:39 , ASP A:40 , HOH A:2020BINDING SITE FOR RESIDUE SO4 A1474
30DC3SOFTWAREHIS B:158 , GLY B:159 , SO4 B:1472BINDING SITE FOR RESIDUE SO4 B1471
31DC4SOFTWARESER A:204 , ALA A:205 , SO4 B:1469 , SO4 B:1472BINDING SITE FOR RESIDUE SO4 A1475
32DC5SOFTWAREASP C:40 , HOH C:2020BINDING SITE FOR RESIDUE SO4 C1471
33DC6SOFTWAREHIS D:158 , GLU D:168 , SO4 D:1470 , HOH D:2152 , HOH D:2268BINDING SITE FOR RESIDUE SO4 D1474
34DC7SOFTWAREHIS A:158 , GLU A:168 , SO4 A:1470BINDING SITE FOR RESIDUE SO4 A1476
35DC8SOFTWAREGLY A:203 , SO4 A:1475 , HIS B:158 , GLU B:168 , LEU B:235 , SO4 B:1469 , SO4 B:1471BINDING SITE FOR RESIDUE SO4 B1472
36DC9SOFTWAREHIS C:158 , GLU C:168 , LEU C:235 , SO4 C:1469 , SO4 C:1470BINDING SITE FOR RESIDUE SO4 C1472
37EC1SOFTWAREGLY D:368 , GLN D:374 , TRP D:376 , SER D:377 , GLU D:408 , TYR D:423 , GLU D:430 , HOH D:2256BINDING SITE FOR RESIDUE MES D1475
38EC2SOFTWAREHIS A:158 , GLY A:159 , HOH A:2066 , HOH A:2067BINDING SITE FOR RESIDUE SO4 A1477
39EC3SOFTWAREALA A:229 , ALA A:230BINDING SITE FOR RESIDUE SO4 A1478
40EC4SOFTWARETRP B:139 , SER B:415 , HOH B:2204BINDING SITE FOR RESIDUE SO4 B1473
41EC5SOFTWAREALA A:48 , SER A:49 , SER A:298 , ASN A:300 , LEU A:349 , THR A:393 , LYS A:410 , THR A:411 , GLY A:412 , THR A:413 , MET A:414 , HOH A:2241BINDING SITE FOR LIGAND IM2 A 500 BOUND TO SER A 49
42EC6SOFTWARESER B:49 , SER B:298 , ASN B:300 , LEU B:349 , THR B:393 , LYS B:410 , THR B:411 , GLY B:412 , THR B:413 , HOH B:2219BINDING SITE FOR LIGAND IM2 B 500 BOUND TO SER B 49
43EC7SOFTWARESER C:49 , SER C:298 , ASN C:300 , LEU C:349 , THR C:393 , LYS C:410 , THR C:411 , GLY C:412 , THR C:413 , HOH C:2218 , HOH C:2233BINDING SITE FOR LIGAND IM2 C 500 BOUND TO SER C 49
44EC8SOFTWAREALA D:48 , SER D:49 , SER D:298 , ASN D:300 , LEU D:349 , LYS D:410 , THR D:411 , GLY D:412 , THR D:413 , HOH D:2033BINDING SITE FOR LIGAND IM2 D 500 BOUND TO SER D 49

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4BEN)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4BEN)

(-) 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:466
 aligned with DAC_ACTSP | P39045 from UniProtKB/Swiss-Prot  Length:538

    Alignment length:466
                                    59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509      
            DAC_ACTSP    50 RLTELREDIDAILEDPALEGAVSGVVVVDTATGEELYSRDGGEQLLPASNMKLFTAAAALEVLGADHSFGTEVAAESAPGRRGEVQDLYLVGRGDPTLSAEDLDAMAAEVAASGVRTVRGDLYADDTWFDSERLVDDWWPEDEPYAYSAQISALTVAHGERFDTGVTEVSVTPAAEGEPADVDLGAAEGYAELDNRAVTGAAGSANTLVIDRPVGTNTIAVTGSLPADAAPVTALRTVDEPAALAGHLFEEALESNGVTVKGDVGLGGVPADWQDAEVLADHTSAELSEILVPFMKFSNNGHAEMLVKSIGQETAGAGTWDAGLVGVEEALSGLGVDTAGLVLNDGSGLSRGNLVTADTVVDLLGQAGSAPWAQTWSASLPVAGESDPFVGGTLANRMRGTAAEGVVEAKTGTMSGVSALSGYVPGPEGELAFSIVNNGHSGPAPLAVQDAIAVRLAEYAGHQAPE 515
               SCOP domains d4bena_ A: D-alanyl-D-alanine carboxypeptidase Dac                                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh..eeeeeeee.....eeeee.......hhhhhhhhhhhhhhhhh......eeeeee........ee..eeeee......hhhhhhhhhhhhhhh...ee...eeee.............hhhhh..hhhh.......ee....ee.eeeeeee........eeehhhhh...eeee..eee........eee......eeeee.eee.....eeeeee..hhhhhhhhhhhhhhhhh..ee...eee..........eeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhhh..hhhhhhhh.......hhhhhhhhh............eeeeeee..eeeeeeee......eeeeeeee......hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ben A   1 RLTELREDIDAILEDPALEGAVSGVVVVDTATGEELYSRDGGEQLLPASNMKLFTAAAALEVLGADHSFGTEVAAESAPGRRGEVQDLYLVGRGDPTLSAEDLDAMAAEVAASGVRTVRGDLYADDTWFDSERLVDDWWPEDEPYAYSAQISALTVAHGERFDTGVTEVSVTPAAEGEPADVDLGAAEGYAELDNRAVTGAAGSANTLVIDRPVGTNTIAVTGSLPADAAPVTALRTVDEPAALAGHLFEEALESNGVTVKGDVGLGGVPADWQDAEVLADHTSAELSEILVPFMKFSNNGHAEMLVKSIGQETAGAGTWDAGLVGVEEALSGLGVDTAGLVLNDGSGLSRGNLVTADTVVDLLGQAGSAPWAQTWSASLPVAGESDPFVGGTLANRMRGTAAEGVVEAKTGTMSGVSALSGYVPGPEGELAFSIVNNGHSGPAPLAVQDAIAVRLAEYAGHQAPE 466
                                    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       330       340       350       360       370       380       390       400       410       420       430       440       450       460      


Chain B from PDB  Type:PROTEIN  Length:466
 aligned with DAC_ACTSP | P39045 from UniProtKB/Swiss-Prot  Length:538

    Alignment length:466
                                    59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509      
            DAC_ACTSP    50 RLTELREDIDAILEDPALEGAVSGVVVVDTATGEELYSRDGGEQLLPASNMKLFTAAAALEVLGADHSFGTEVAAESAPGRRGEVQDLYLVGRGDPTLSAEDLDAMAAEVAASGVRTVRGDLYADDTWFDSERLVDDWWPEDEPYAYSAQISALTVAHGERFDTGVTEVSVTPAAEGEPADVDLGAAEGYAELDNRAVTGAAGSANTLVIDRPVGTNTIAVTGSLPADAAPVTALRTVDEPAALAGHLFEEALESNGVTVKGDVGLGGVPADWQDAEVLADHTSAELSEILVPFMKFSNNGHAEMLVKSIGQETAGAGTWDAGLVGVEEALSGLGVDTAGLVLNDGSGLSRGNLVTADTVVDLLGQAGSAPWAQTWSASLPVAGESDPFVGGTLANRMRGTAAEGVVEAKTGTMSGVSALSGYVPGPEGELAFSIVNNGHSGPAPLAVQDAIAVRLAEYAGHQAPE 515
               SCOP domains d4benb_ B: D-alanyl-D-alanine carboxypeptidase Dac                                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh..eeeeeeee.....eeeee.......hhhhhhhhhhhhhhhhhh.....eeeeee........ee..eeeee......hhhhhhhhhhhhhhh...ee...eeee.............hhhhh..hhhh.......ee....ee.eeeeeee........eeehhhhh...eeeeeeeee........eee......eeeeeeeee.....eeeeee..hhhhhhhhhhhhhhhhh..ee...eee..........eeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhhh..hhhhhhhhh......hhhhhhhhh............eeeeeee..eeeeeeee......eeeeeeee......hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ben B   1 RLTELREDIDAILEDPALEGAVSGVVVVDTATGEELYSRDGGEQLLPASNMKLFTAAAALEVLGADHSFGTEVAAESAPGRRGEVQDLYLVGRGDPTLSAEDLDAMAAEVAASGVRTVRGDLYADDTWFDSERLVDDWWPEDEPYAYSAQISALTVAHGERFDTGVTEVSVTPAAEGEPADVDLGAAEGYAELDNRAVTGAAGSANTLVIDRPVGTNTIAVTGSLPADAAPVTALRTVDEPAALAGHLFEEALESNGVTVKGDVGLGGVPADWQDAEVLADHTSAELSEILVPFMKFSNNGHAEMLVKSIGQETAGAGTWDAGLVGVEEALSGLGVDTAGLVLNDGSGLSRGNLVTADTVVDLLGQAGSAPWAQTWSASLPVAGESDPFVGGTLANRMRGTAAEGVVEAKTGTMSGVSALSGYVPGPEGELAFSIVNNGHSGPAPLAVQDAIAVRLAEYAGHQAPE 466
                                    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       330       340       350       360       370       380       390       400       410       420       430       440       450       460      


Chain C from PDB  Type:PROTEIN  Length:466
 aligned with DAC_ACTSP | P39045 from UniProtKB/Swiss-Prot  Length:538

    Alignment length:466
                                    59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509      
            DAC_ACTSP    50 RLTELREDIDAILEDPALEGAVSGVVVVDTATGEELYSRDGGEQLLPASNMKLFTAAAALEVLGADHSFGTEVAAESAPGRRGEVQDLYLVGRGDPTLSAEDLDAMAAEVAASGVRTVRGDLYADDTWFDSERLVDDWWPEDEPYAYSAQISALTVAHGERFDTGVTEVSVTPAAEGEPADVDLGAAEGYAELDNRAVTGAAGSANTLVIDRPVGTNTIAVTGSLPADAAPVTALRTVDEPAALAGHLFEEALESNGVTVKGDVGLGGVPADWQDAEVLADHTSAELSEILVPFMKFSNNGHAEMLVKSIGQETAGAGTWDAGLVGVEEALSGLGVDTAGLVLNDGSGLSRGNLVTADTVVDLLGQAGSAPWAQTWSASLPVAGESDPFVGGTLANRMRGTAAEGVVEAKTGTMSGVSALSGYVPGPEGELAFSIVNNGHSGPAPLAVQDAIAVRLAEYAGHQAPE 515
               SCOP domains d4benc_ C: D-alanyl-D-alanine carboxypeptidase Dac                                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.hhhhh..eeeeeeee.....eeeee.......hhhhhhhhhhhhhhhhhh.....eeeeee........ee..eeeee......hhhhhhhhhhhhhhh...ee...eeee.............hhhhh..hhhh.......ee....ee.eeeeeee........eeehhhhh...eeeeeeeee........eee......eeeeeeeee.....eeeeee..hhhhhhhhhhhhhhhhh..ee...eee..........eeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhh...hhhhhhhhh......hhhhhhhhh............eeeeeee..eeeeeeee......eeeeeeee......hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ben C   1 RLTELREDIDAILEDPALEGAVSGVVVVDTATGEELYSRDGGEQLLPASNMKLFTAAAALEVLGADHSFGTEVAAESAPGRRGEVQDLYLVGRGDPTLSAEDLDAMAAEVAASGVRTVRGDLYADDTWFDSERLVDDWWPEDEPYAYSAQISALTVAHGERFDTGVTEVSVTPAAEGEPADVDLGAAEGYAELDNRAVTGAAGSANTLVIDRPVGTNTIAVTGSLPADAAPVTALRTVDEPAALAGHLFEEALESNGVTVKGDVGLGGVPADWQDAEVLADHTSAELSEILVPFMKFSNNGHAEMLVKSIGQETAGAGTWDAGLVGVEEALSGLGVDTAGLVLNDGSGLSRGNLVTADTVVDLLGQAGSAPWAQTWSASLPVAGESDPFVGGTLANRMRGTAAEGVVEAKTGTMSGVSALSGYVPGPEGELAFSIVNNGHSGPAPLAVQDAIAVRLAEYAGHQAPE 466
                                    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       330       340       350       360       370       380       390       400       410       420       430       440       450       460      


Chain D from PDB  Type:PROTEIN  Length:466
 aligned with DAC_ACTSP | P39045 from UniProtKB/Swiss-Prot  Length:538

    Alignment length:466
                                    59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509      
            DAC_ACTSP    50 RLTELREDIDAILEDPALEGAVSGVVVVDTATGEELYSRDGGEQLLPASNMKLFTAAAALEVLGADHSFGTEVAAESAPGRRGEVQDLYLVGRGDPTLSAEDLDAMAAEVAASGVRTVRGDLYADDTWFDSERLVDDWWPEDEPYAYSAQISALTVAHGERFDTGVTEVSVTPAAEGEPADVDLGAAEGYAELDNRAVTGAAGSANTLVIDRPVGTNTIAVTGSLPADAAPVTALRTVDEPAALAGHLFEEALESNGVTVKGDVGLGGVPADWQDAEVLADHTSAELSEILVPFMKFSNNGHAEMLVKSIGQETAGAGTWDAGLVGVEEALSGLGVDTAGLVLNDGSGLSRGNLVTADTVVDLLGQAGSAPWAQTWSASLPVAGESDPFVGGTLANRMRGTAAEGVVEAKTGTMSGVSALSGYVPGPEGELAFSIVNNGHSGPAPLAVQDAIAVRLAEYAGHQAPE 515
               SCOP domains d4bend_ D: D-alanyl-D-alanine carboxypeptidase Dac                                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh..eeeeeeee.....eeeee.......hhhhhhhhhhhhhhhhh......eeeeee........ee..eeeee......hhhhhhhhhhhhhhh...ee...eeee.............hhhhh..hhhh.......ee....ee.eeeeeee........eeehhhhh...eeee..eee........eee......eeeee.eee.....eeeeee..hhhhhhhhhhhhhhhhh..ee...eee..........eeeeeee..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhhh..hhhhhhh........hhhhhhhhh............eeeeeee..eeeeeeeee....eeeeeeeee......hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ben D   1 RLTELREDIDAILEDPALEGAVSGVVVVDTATGEELYSRDGGEQLLPASNMKLFTAAAALEVLGADHSFGTEVAAESAPGRRGEVQDLYLVGRGDPTLSAEDLDAMAAEVAASGVRTVRGDLYADDTWFDSERLVDDWWPEDEPYAYSAQISALTVAHGERFDTGVTEVSVTPAAEGEPADVDLGAAEGYAELDNRAVTGAAGSANTLVIDRPVGTNTIAVTGSLPADAAPVTALRTVDEPAALAGHLFEEALESNGVTVKGDVGLGGVPADWQDAEVLADHTSAELSEILVPFMKFSNNGHAEMLVKSIGQETAGAGTWDAGLVGVEEALSGLGVDTAGLVLNDGSGLSRGNLVTADTVVDLLGQAGSAPWAQTWSASLPVAGESDPFVGGTLANRMRGTAAEGVVEAKTGTMSGVSALSGYVPGPEGELAFSIVNNGHSGPAPLAVQDAIAVRLAEYAGHQAPE 466
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 Classification and Annotation

(-) SCOP Domains  (1, 4)

Asymmetric Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (DAC_ACTSP | P39045)
molecular function
    GO:0004180    carboxypeptidase activity    Catalysis of the hydrolysis of the terminal or penultimate peptide bond at the C-terminal end of a peptide or polypeptide.
    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.
    GO:0009002    serine-type D-Ala-D-Ala carboxypeptidase activity    Catalysis of the reaction: (Ac)2-L-Lys-D-alanyl-D-alanine + H2O = (Ac)2-L-Lys-D-alanine + D-alanine.
    GO:0004185    serine-type carboxypeptidase activity    Catalysis of the hydrolysis of a peptide bond not more than three residues from the C-terminus of a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0071555    cell wall organization    A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
    GO:0009252    peptidoglycan biosynthetic process    The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
    GO:0046677    response to antibiotic    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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  4ben
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  DAC_ACTSP | P39045
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  3.4.16.4
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 Related Entries

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

UniProtKB/Swiss-Prot
        DAC_ACTSP | P39045: 1w79 1w8q 1w8y 2vgj 2vgk 2wke 2xdm 2xk1 2xln 2y4a 2y55 2y59 3zcz 3zvt 3zvw 4b4x 4b4z

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4BEN)