3ZVW - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   UNEXPECTED TRICOVALENT BINDING MODE OF BORONIC ACIDS WITHIN THE ACTIVE SITE OF A PENICILLIN BINDING PROTEIN

Authors :   E. Sauvage, A. Zervosen, R. Herman, F. Kerff, M. Rocaboy, P. Charlier

Date :   28 Jul 11 (Deposition) - 29 Feb 12 (Release) - 29 Feb 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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, Peptidoglycan, Penicillin-Binding, Tetravalent Boron (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Zervosen, R. Herman, F. Kerff, A. Herman, A. Bouillez, F. Prati, R. F. Pratt, J. M. Frere, B. Joris, A. Luxen, P. Charlier, E. Sauvage
Unexpected Tricovalent Binding Mode Of Boronic Acids Within The Active Site Of A Penicillin- Binding Protein.
J. Am. Chem. Soc. V. 133 10839 2011
PubMed-ID: 21574608 | Reference-DOI: 10.1021/JA200696Y

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

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
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)

Asymmetric Unit (6, 39)

No.	Name	Count	Type	Full Name
1	33D	2	Ligand/Ion	3,3-DIMETHYLBUTAN-1-OL
2	ACN	2	Ligand/Ion	ACETONE
3	FP5	2	Ligand/Ion	PHENYLACETAMIDOMETHYL BORONIC ACID
4	MES	1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
5	MG	14	Ligand/Ion	MAGNESIUM ION
6	SO4	18	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 5)

No.	Name	Count	Type	Full Name
1	33D	-1	Ligand/Ion	3,3-DIMETHYLBUTAN-1-OL
2	ACN	-1	Ligand/Ion	ACETONE
3	FP5	-1	Ligand/Ion	PHENYLACETAMIDOMETHYL BORONIC ACID
4	MES	-1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
5	MG	-1	Ligand/Ion	MAGNESIUM ION
6	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 2 (4, 7)

No.	Name	Count	Type	Full Name
1	33D	1	Ligand/Ion	3,3-DIMETHYLBUTAN-1-OL
2	ACN	1	Ligand/Ion	ACETONE
3	FP5	1	Ligand/Ion	PHENYLACETAMIDOMETHYL BORONIC ACID
4	MES	-1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
5	MG	-1	Ligand/Ion	MAGNESIUM ION
6	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 3 (4, 7)

No.	Name	Count	Type	Full Name
1	33D	1	Ligand/Ion	3,3-DIMETHYLBUTAN-1-OL
2	ACN	1	Ligand/Ion	ACETONE
3	FP5	1	Ligand/Ion	PHENYLACETAMIDOMETHYL BORONIC ACID
4	MES	-1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
5	MG	-1	Ligand/Ion	MAGNESIUM ION
6	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 4 (2, 6)

No.	Name	Count	Type	Full Name
1	33D	-1	Ligand/Ion	3,3-DIMETHYLBUTAN-1-OL
2	ACN	-1	Ligand/Ion	ACETONE
3	FP5	-1	Ligand/Ion	PHENYLACETAMIDOMETHYL BORONIC ACID
4	MES	1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
5	MG	-1	Ligand/Ion	MAGNESIUM ION
6	SO4	5	Ligand/Ion	SULFATE ION

Asymmetric Unit (35, 35)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	SER A:49 , SER A:298 , THR A:393 , LYS A:410 , THR A:411 , GLY A:412 , THR A:413 , HOH A:2049 , HOH A:2448 , HOH A:2474	BINDING SITE FOR RESIDUE SO4 A 600
02	AC2	SOFTWARE	HIS A:282 , THR A:283 , HOH A:2151 , HOH A:2152 , HOH A:2359 , HOH A:2361	BINDING SITE FOR RESIDUE SO4 A 601
03	AC3	SOFTWARE	ALA A:234 , ARG A:236 , HOH A:2475	BINDING SITE FOR RESIDUE SO4 A 602
04	AC4	SOFTWARE	SER A:131 , ARG A:133 , LEU A:134 , HOH A:2231	BINDING SITE FOR RESIDUE SO4 A 603
05	AC5	SOFTWARE	GLY A:159 , GLU A:160 , ARG A:161 , HOH A:2238 , HOH A:2479	BINDING SITE FOR RESIDUE SO4 A 604
06	AC6	SOFTWARE	ALA A:186 , GLU A:188 , HIS A:247 , GLU A:251	BINDING SITE FOR RESIDUE MG A 610
07	AC7	SOFTWARE	ALA A:402 , VAL A:406 , HIS A:462 , GLN A:463 , HOH A:2441	BINDING SITE FOR RESIDUE MG A 611
08	AC8	SOFTWARE	HOH A:2080	BINDING SITE FOR RESIDUE MG A1469
09	AC9	SOFTWARE	ALA B:48 , SER B:49 , SER B:298 , ASN B:300 , GLY B:348 , LEU B:349 , LYS B:410 , THR B:411 , GLY B:412 , THR B:413 , HOH B:2442	BINDING SITE FOR RESIDUE FP5 B 500
10	BC1	SOFTWARE	HIS B:282 , THR B:283 , HOH B:2178 , HOH B:2366	BINDING SITE FOR RESIDUE SO4 B 601
11	BC2	SOFTWARE	ARG B:236 , HOH B:2473 , HOH B:2474	BINDING SITE FOR RESIDUE SO4 B 602
12	BC3	SOFTWARE	SER B:131 , ARG B:133 , LEU B:134 , HOH B:2209 , HOH B:2252 , HOH B:2476	BINDING SITE FOR RESIDUE SO4 B 603
13	BC4	SOFTWARE	GLY B:159 , GLU B:160 , ARG B:161 , HOH B:2262 , HOH B:2264 , HOH B:2269 , HOH B:2478	BINDING SITE FOR RESIDUE SO4 B 604
14	BC5	SOFTWARE	HOH B:2480 , TRP C:139 , ARG C:351 , MET C:414 , SER C:415 , HOH C:2489	BINDING SITE FOR RESIDUE 33D B 620
15	BC6	SOFTWARE	HOH B:2481	BINDING SITE FOR RESIDUE MG B1467
16	BC7	SOFTWARE	ASP B:40	BINDING SITE FOR RESIDUE MG B3001
17	BC8	SOFTWARE	ALA C:48 , SER C:49 , SER C:298 , ASN C:300 , GLY C:348 , LEU C:349 , LYS C:410 , THR C:411 , GLY C:412 , THR C:413 , ACN C:610 , HOH C:2484	BINDING SITE FOR RESIDUE FP5 C 500
18	BC9	SOFTWARE	HIS C:282 , THR C:283 , HOH C:2185 , HOH C:2397 , HOH C:2400	BINDING SITE FOR RESIDUE SO4 C 601
19	CC1	SOFTWARE	ARG C:236 , HOH C:2523	BINDING SITE FOR RESIDUE SO4 C 602
20	CC2	SOFTWARE	SER C:131 , GLU C:132 , ARG C:133 , LEU C:134 , HOH C:2216 , HOH C:2222 , HOH C:2261 , HOH C:2525	BINDING SITE FOR RESIDUE SO4 C 603
21	CC3	SOFTWARE	HIS C:158 , GLY C:159 , GLU C:160 , ARG C:161 , HOH C:2270 , HOH C:2278 , HOH C:2528	BINDING SITE FOR RESIDUE SO4 C 604
22	CC4	SOFTWARE	THR C:413 , FP5 C:500 , HOH C:2242 , HOH C:2529	BINDING SITE FOR RESIDUE ACN C 610
23	CC5	SOFTWARE	TRP B:139 , MET B:414 , SER B:415	BINDING SITE FOR RESIDUE 33D C 620
24	CC6	SOFTWARE	ARG C:455	BINDING SITE FOR RESIDUE MG C1467
25	CC7	SOFTWARE	VAL C:214	BINDING SITE FOR RESIDUE MG C1468
26	CC8	SOFTWARE	GLN C:312 , GLY C:316	BINDING SITE FOR RESIDUE MG C1469
27	CC9	SOFTWARE	ASP C:40	BINDING SITE FOR RESIDUE MG C3001
28	DC1	SOFTWARE	SER D:49 , SER D:298 , THR D:393 , LYS D:410 , THR D:411 , GLY D:412 , THR D:413 , HOH D:2066 , HOH D:2436	BINDING SITE FOR RESIDUE SO4 D 600
29	DC2	SOFTWARE	HIS D:282 , THR D:283 , HOH D:2338 , HOH D:2339	BINDING SITE FOR RESIDUE SO4 D 601
30	DC3	SOFTWARE	ALA D:234 , ARG D:236 , HOH D:2308 , HOH D:2461	BINDING SITE FOR RESIDUE SO4 D 602
31	DC4	SOFTWARE	SER D:131 , GLU D:132 , ARG D:133 , LEU D:134 , HOH D:2186 , HOH D:2229	BINDING SITE FOR RESIDUE SO4 D 603
32	DC5	SOFTWARE	GLY D:159 , GLU D:160 , ARG D:161 , HOH D:2237 , HOH D:2243 , HOH D:2463	BINDING SITE FOR RESIDUE SO4 D 604
33	DC6	SOFTWARE	ALA D:186 , GLU D:188 , GLU D:251	BINDING SITE FOR RESIDUE MG D 610
34	DC7	SOFTWARE	VAL D:406 , HIS D:462	BINDING SITE FOR RESIDUE MG D 611
35	DC8	SOFTWARE	GLY D:368 , GLN D:374 , TRP D:376 , SER D:377 , GLU D:408 , TYR D:423 , GLU D:430	BINDING SITE FOR RESIDUE MES D1469

(no "SS Bond" information available for 3ZVW)

(no "Cis Peptide Bond" information available for 3ZVW)

(no "SAP(SNP)/Variant" information available for 3ZVW)

(no "PROSITE Motif" information available for 3ZVW)

(no "Exon" information available for 3ZVW)

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 d3zvwa_ 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..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhh..hhhhhhhh.......hhhhhhhhh............eeeeeee..eeeeeeee......eeeeeeee......hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zvw 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 d3zvwb_ B: 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..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhhh..hhhhhhhhh......hhhhhhhhh............eee..ee..eeeeeeee......eeeeeeee......hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zvw 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 d3zvwc_ C: 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...eeeeeeeee........eee......eeeeeeeee.....eeeeee..hhhhhhhhhhhhhhhhh..ee...eee..........eeeeeee..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhhh..hhhhhhhhh......hhhhhhhhh............eee..ee..eeeeeeee......eeeeeeee......hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zvw 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 d3zvwd_ D: 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........eeehhhh....eeee..eee........eee......eeeee.eee.....eeeeee..hhhhhhhhhhhhhhhhh..ee...eee..........eeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhhhh.hhhhhhh........hhhhhhhhh............eeeeeee..eeeeeeee......eeeeeeee......hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zvw D   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

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: beta-lactamase/transpeptidase-like (515)

Superfamily: beta-lactamase/transpeptidase-like (515)

Family: Dac-like (29)

Protein domain: D-alanyl-D-alanine carboxypeptidase Dac (17)

Actinomadura sp. [TaxId: 1989] (17)

1a	d3zvwa_	A:
1b	d3zvwb_	B:
1c	d3zvwc_	C:
1d	d3zvwd_	D:

(no "CATH Domain" information available for 3ZVW)

(no "Pfam Domain" information available for 3ZVW)

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.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3zvw)

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	3zvw
		Family and Domain Information	:	ProDom \| SYSTERS
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	DAC_ACTSP \| P39045
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Access by Enzyme Classificator (EC Number)
	3.4.16.4
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	DAC_ACTSP \| P39045
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1w79	CRYSTAL STRUCTURE OF THE DD-TRANSPEPTIDASE- CARBOXYPEPTIDASE FROM ACTINOMADURA R39
1w8q	CRYSTAL STRUCTURE OF THE DD-PEPTIDASE FROM ACTINOMADURA R39 WITH COBALT IONS
1w8y	CRYSTAL STRUCTURE OF THE NITROCEFIN ACYL-DD-PEPTIDASE FROM ACTINOMADURA R39.
2vgj	CRYSTAL STRUCTURE OF ACTINOMADURA R39 DD-PEPTIDASE COMPLEXED WITH A PEPTIDOGLYCAN-MIMETIC CEPHALOSPORIN
2vgk	CRYSTAL STRUCTURE OF ACTINOMADURA R39 DD-PEPTIDASE COMPLEXED WITH A PEPTIDOGLYCAN-MIMETIC CEPHALOSPORIN
2wke	CRYSTAL STRUCTURE OF THE ACTINOMADURA R39 DD-PEPTIDASE INHIBITED BY 6-BETA-IODOPENICILLANATE.
2xdm	CRYSTAL STRUCTURE OF A COMPLEX BETWEEN ACTINOMADURA R39 DD-PEPTIDASE AND A PEPTIDOGLYCAN MIMETIC BORONATE INHIBITOR
2xk1	CRYSTAL STRUCTURE OF A COMPLEX BETWEEN ACTINOMADURA R39 DD-PEPTIDASE AND A BORONATE INHIBITOR
2xln	CRYSTAL STRUCTURE OF A COMPLEX BETWEEN ACTINOMADURA R39 DD-PEPTIDASE AND A BORONATE INHIBITOR
2y4a	UNEXPECTED TRICOVALENT BINDING MODE OF BORONIC ACIDS WITHIN THE ACTIVE SITE OF A PENICILLIN BINDING PROTEIN
2y55	UNEXPECTED TRICOVALENT BINDING MODE OF BORONIC ACIDS WITHIN THE ACTIVE SITE OF A PENICILLIN BINDING PROTEIN
2y59	UNEXPECTED TRICOVALENT BINDING MODE OF BORONIC ACIDS WITHIN THE ACTIVE SITE OF A PENICILLIN BINDING PROTEIN
3zvt	UNEXPECTED TRICOVALENT BINDING MODE OF BORONIC ACIDS WITHIN THE ACTIVE SITE OF A PENICILLIN BINDING PROTEIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 39)

Sites (35, 35)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (11, 11)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File