2XDM - 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 :   CRYSTAL STRUCTURE OF A COMPLEX BETWEEN ACTINOMADURA R39 DD PEPTIDASE AND A PEPTIDOGLYCAN MIMETIC BORONATE INHIBITOR

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

Date :   04 May 10 (Deposition) - 21 Jul 10 (Release) - 23 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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-Inhibitor Complex, Boronic Acid, Peptidoglycan, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Dzhekieva, M. Rocaboy, F. Kerff, P. Charlier, E. Sauvage, R. F. Prat
Crystal Structure Of A Complex Between The Actinomadura R39 Dd-Peptidase And A Peptidoglycan- Mimetic Boronate Inhibitor: Interpretation Of A Transition State Analogue In Terms Of Catalytic Mechanism.
Biochemistry V. 49 6411 2010
PubMed-ID: 20608745 | Reference-DOI: 10.1021/BI100757C

Molecule 1 - D-ALANYL-D-ALANINE CARBOXYPEPTIDASE
	Chains	:	A, B, C, D
	EC Number	:	3.4.16.4
	Organism Scientific	:	ACTINOMADURA
	Organism Taxid	:	72570
	Strain	:	R39
	Synonym	:	DD-PEPTIDASE, DD-CARBOXYPEPTIDASE, 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 (4, 27)

No.	Name	Count	Type	Full Name
1	BO8	2	Ligand/Ion	(D-ALPHA-AMINOPIMELYLAMINO)-D-1-ETHYLBORONICACID
2	CO	4	Ligand/Ion	COBALT (II) ION
3	MES	1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4	SO4	20	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 5)

No.	Name	Count	Type	Full Name
1	BO8	-1	Ligand/Ion	(D-ALPHA-AMINOPIMELYLAMINO)-D-1-ETHYLBORONICACID
2	CO	-1	Ligand/Ion	COBALT (II) ION
3	MES	-1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 6)

No.	Name	Count	Type	Full Name
1	BO8	1	Ligand/Ion	(D-ALPHA-AMINOPIMELYLAMINO)-D-1-ETHYLBORONICACID
2	CO	-1	Ligand/Ion	COBALT (II) ION
3	MES	-1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 3 (2, 6)

No.	Name	Count	Type	Full Name
1	BO8	1	Ligand/Ion	(D-ALPHA-AMINOPIMELYLAMINO)-D-1-ETHYLBORONICACID
2	CO	-1	Ligand/Ion	COBALT (II) ION
3	MES	-1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 4 (2, 6)

No.	Name	Count	Type	Full Name
1	BO8	-1	Ligand/Ion	(D-ALPHA-AMINOPIMELYLAMINO)-D-1-ETHYLBORONICACID
2	CO	-1	Ligand/Ion	COBALT (II) ION
3	MES	1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
4	SO4	5	Ligand/Ion	SULFATE ION

Asymmetric Unit (27, 27)

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	BINDING SITE FOR RESIDUE SO4 A 600
02	AC2	SOFTWARE	ASP A:281 , HIS A:282 , THR A:283 , HOH A:2178	BINDING SITE FOR RESIDUE SO4 A 601
03	AC3	SOFTWARE	ARG A:236 , HOH A:2179	BINDING SITE FOR RESIDUE SO4 A 602
04	AC4	SOFTWARE	SER A:131 , ARG A:133 , LEU A:134	BINDING SITE FOR RESIDUE SO4 A 603
05	AC5	SOFTWARE	GLY A:159 , GLU A:160 , ARG A:161 , HOH A:2073 , HOH A:2181	BINDING SITE FOR RESIDUE SO4 A 604
06	AC6	SOFTWARE	GLU A:188 , HIS A:247 , GLU A:251	BINDING SITE FOR RESIDUE CO A 610
07	AC7	SOFTWARE	ALA A:402 , VAL A:406 , HIS A:462 , GLN A:463	BINDING SITE FOR RESIDUE CO A 611
08	AC8	SOFTWARE	ALA B:48 , SER B:49 , TRP B:139 , ASP B:142 , TYR B:147 , SER B:298 , ASN B:300 , GLY B:348 , LEU B:349 , ARG B:351 , GLY B:412 , THR B:413 , MET B:414 , SER B:415 , SO4 B:600 , HOH B:2110 , HOH B:2111	BINDING SITE FOR RESIDUE BO8 B 500
09	AC9	SOFTWARE	SER B:298 , THR B:393 , LYS B:410 , THR B:411 , GLY B:412 , THR B:413 , BO8 B:500	BINDING SITE FOR RESIDUE SO4 B 600
10	BC1	SOFTWARE	HIS B:282 , THR B:283 , HOH B:2113	BINDING SITE FOR RESIDUE SO4 B 601
11	BC2	SOFTWARE	ARG B:236 , HOH B:2115 , HOH B:2117	BINDING SITE FOR RESIDUE SO4 B 602
12	BC3	SOFTWARE	GLU B:132 , ARG B:133 , LEU B:134	BINDING SITE FOR RESIDUE SO4 B 603
13	BC4	SOFTWARE	GLY B:159 , GLU B:160 , ARG B:161 , HOH B:2049 , HOH B:2119	BINDING SITE FOR RESIDUE SO4 B 604
14	BC5	SOFTWARE	SER C:49 , LYS C:52 , TRP C:139 , ASP C:142 , TYR C:147 , SER C:298 , ASN C:300 , SER C:347 , GLY C:348 , LEU C:349 , ARG C:351 , GLY C:412 , THR C:413 , SER C:415 , SO4 C:600 , HOH C:2142	BINDING SITE FOR RESIDUE BO8 C 500
15	BC6	SOFTWARE	SER C:298 , LYS C:410 , THR C:411 , GLY C:412 , THR C:413 , BO8 C:500	BINDING SITE FOR RESIDUE SO4 C 600
16	BC7	SOFTWARE	ASP C:281 , HIS C:282 , THR C:283	BINDING SITE FOR RESIDUE SO4 C 601
17	BC8	SOFTWARE	ARG C:236	BINDING SITE FOR RESIDUE SO4 C 602
18	BC9	SOFTWARE	SER C:131 , ARG C:133 , LEU C:134	BINDING SITE FOR RESIDUE SO4 C 603
19	CC1	SOFTWARE	GLY C:159 , GLU C:160 , ARG C:161	BINDING SITE FOR RESIDUE SO4 C 604
20	CC2	SOFTWARE	SER D:49 , SER D:298 , THR D:393 , LYS D:410 , THR D:411 , GLY D:412 , THR D:413	BINDING SITE FOR RESIDUE SO4 D 600
21	CC3	SOFTWARE	ASP D:281 , HIS D:282 , THR D:283	BINDING SITE FOR RESIDUE SO4 D 601
22	CC4	SOFTWARE	ALA D:234 , ARG D:236 , HOH D:2110	BINDING SITE FOR RESIDUE SO4 D 602
23	CC5	SOFTWARE	SER D:131 , GLU D:132 , ARG D:133 , LEU D:134 , HOH D:2111 , HOH D:2112 , HOH D:2113	BINDING SITE FOR RESIDUE SO4 D 603
24	CC6	SOFTWARE	GLY D:159 , GLU D:160 , ARG D:161	BINDING SITE FOR RESIDUE SO4 D 604
25	CC7	SOFTWARE	GLU D:188 , HIS D:247 , GLU D:251	BINDING SITE FOR RESIDUE CO D 610
26	CC8	SOFTWARE	VAL D:406 , HIS D:462	BINDING SITE FOR RESIDUE CO D 611
27	CC9	SOFTWARE	ALA D:373 , TRP D:376 , SER D:377 , TYR D:423 , GLU D:430	BINDING SITE FOR RESIDUE MES D1467

(no "SS Bond" information available for 2XDM)

(no "Cis Peptide Bond" information available for 2XDM)

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

(no "PROSITE Motif" information available for 2XDM)

(no "Exon" information available for 2XDM)

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 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2xdmA01 A:1-68,A:285-466 DD-peptidase/beta-lactamase superfamily    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------2xdmA01 A:1-68,A:285-466 DD-peptidase/beta-lactamase superfamily                                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh..eeeeeeee.....eeeee....ee.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....................eehhhhhhhhhhhhh..hhhhhhhhh......hhhhhhhhh............eeeeeee..eeeeeeee......eeeeeeee......hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xdm 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 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2xdmB01 B:1-68,B:285-466 DD-peptidase/beta-lactamase superfamily    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------2xdmB01 B:1-68,B:285-466 DD-peptidase/beta-lactamase superfamily                                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh..eeeeeeee.......eee.......hhhhhhhhhhhhhhhhh......eeeeee........ee..eeeee......hhhhhhhhhhhhhh....ee...eeee.............hhhhh.hhhhh.......ee....ee.eeeeeee........eeehhhhh...eeee..eee........eee......eeeee.eee.....eeeeee..hhhhhhhhhhhhhhhhh..ee...eee..........eeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhhhh.hhhhhhhh.......hhhhhhhhh............eeeeeee..eeeeeeee......eeeeeeee......hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xdm 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:465
 aligned with DAC_ACTSP | P39045 from UniProtKB/Swiss-Prot  Length:538

    Alignment length:465
                                    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 RLTELREDIDAILEDPALEGAVSGVVVVDTATGEELYSRDGGEQLLPASNMKLFTAAAALEVLGADHSFGTEVAAESAPGRRGEVQDLYLVGRGDPTLSAEDLDAMAAEVAASGVRTVRGDLYADDTWFDSERLVDDWWPEDEPYAYSAQISALTVAHGERFDTGVTEVSVTPAAEGEPADVDLGAAEGYAELDNRAVTGAAGSANTLVIDRPVGTNTIAVTGSLPADAAPVTALRTVDEPAALAGHLFEEALESNGVTVKGDVGLGGVPADWQDAEVLADHTSAELSEILVPFMKFSNNGHAEMLVKSIGQETAGAGTWDAGLVGVEEALSGLGVDTAGLVLNDGSGLSRGNLVTADTVVDLLGQAGSAPWAQTWSASLPVAGESDPFVGGTLANRMRGTAAEGVVEAKTGTMSGVSALSGYVPGPEGELAFSIVNNGHSGPAPLAVQDAIAVRLAEYAGHQAP 514
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2xdmC01 C:1-68,C:285-465 DD-peptidase/beta-lactamase superfamily    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------2xdmC01 C:1-68,C:285-465 DD-peptidase/beta-lactamase superfamily                                                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh..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.....................hhhhhhhhhhhhh...hhhhhhhhh......hhhhhhhhh............eeeeeee..eeeeeeee......eeeeeeee......hhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xdm C   1 RLTELREDIDAILEDPALEGAVSGVVVVDTATGEELYSRDGGEQLLPASNMKLFTAAAALEVLGADHSFGTEVAAESAPGRRGEVQDLYLVGRGDPTLSAEDLDAMAAEVAASGVRTVRGDLYADDTWFDSERLVDDWWPEDEPYAYSAQISALTVAHGERFDTGVTEVSVTPAAEGEPADVDLGAAEGYAELDNRAVTGAAGSANTLVIDRPVGTNTIAVTGSLPADAAPVTALRTVDEPAALAGHLFEEALESNGVTVKGDVGLGGVPADWQDAEVLADHTSAELSEILVPFMKFSNNGHAEMLVKSIGQETAGAGTWDAGLVGVEEALSGLGVDTAGLVLNDGSGLSRGNLVTADTVVDLLGQAGSAPWAQTWSASLPVAGESDPFVGGTLANRMRGTAAEGVVEAKTGTMSGVSALSGYVPGPEGELAFSIVNNGHSGPAPLAVQDAIAVRLAEYAGHQAP 465
                                    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 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2xdmD01 D:1-68,D:285-466 DD-peptidase/beta-lactamase superfamily    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------2xdmD01 D:1-68,D:285-466 DD-peptidase/beta-lactamase superfamily                                                                                                                       CATH domains
           Pfam domains (1) ----Peptidase_S13-2xdmD01 D:5-459                                                                                                                                                                                                                                                                                                                                                                                                                                          ------- Pfam domains (1)
           Pfam domains (2) ----Peptidase_S13-2xdmD02 D:5-459                                                                                                                                                                                                                                                                                                                                                                                                                                          ------- Pfam domains (2)
           Pfam domains (3) ----Peptidase_S13-2xdmD03 D:5-459                                                                                                                                                                                                                                                                                                                                                                                                                                          ------- Pfam domains (3)
           Pfam domains (4) ----Peptidase_S13-2xdmD04 D:5-459                                                                                                                                                                                                                                                                                                                                                                                                                                          ------- Pfam domains (4)
         Sec.struct. author hhhhhhhhhhhhhhhhhhh..eeeeeeee....eeeeee.......hhhhhhhhhhhhhhhhh......eeeeee........ee..eeeee......hhhhhhhhhhhhhhhh..ee...eeee.............hhhhh..hhhh.......ee....ee.eeeeeee........eeehhhh....eeee..eee........eee......eeeee.eee.....eeeeee..hhhhhhhhhhhhhhhhh..ee...eee..........eeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhhhh.hhhhhhh........hhhhhhhhh............eee..ee..eeeeeeeee....eeeeeeeee......hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xdm 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 '\|'

(no "SCOP Domain" information available for 2XDM)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Beta-lactamase (339)

Homologous Superfamily: DD-peptidase/beta-lactamase superfamily (335)

Actinomadura. Organism_taxid: 72570. Strain: r39 (1)

1a	2xdmA01	A:1-68,A:285-466
1b	2xdmB01	B:1-68,B:285-466
1c	2xdmD01	D:1-68,D:285-466
1d	2xdmC01	C:1-68,C:285-465

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Beta-lactamase (210)

Family: Peptidase_S13 (9)

Actinomadura sp. (strain R39) (8)

1a	Peptidase_S13-2xdmD01	D:5-459
1b	Peptidase_S13-2xdmD02	D:5-459
1c	Peptidase_S13-2xdmD03	D:5-459
1d	Peptidase_S13-2xdmD04	D:5-459

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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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
2wix	CRYSTAL STRUCTURE OF ACTINOMADURA R39 DD- CARBOXYPEPTIDASE COMPLEXED WITH THE SQ26445 MONOBACTAM
2wke	CRYSTAL STRUCTURE OF THE ACTINOMADURA R39 DD -PEPTIDASE INHIBITED BY 6-BETA- IODOPENICILLANATE.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 27)

Sites (27, 27)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (1, 4)

Pfam Domains (1, 4)

Gene Ontology (11, 11)

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