3ITB - 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 PENICILLIN-BINDING PROTEIN 6 (PBP6) FROM E. COLI IN COMPLEX WITH A SUBSTRATE FRAGMENT

Authors :   Y. Chen, W. Zhang, Q. Shi, D. Hesek, M. Lee, S. Mobashery, B. K. Shoichet

Date :   27 Aug 09 (Deposition) - 20 Oct 09 (Release) - 27 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym. Unit : A,B,C,D,L
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C,L  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Penicillin-Binding Protein, Pbp6, Dd-Carboxypeptidase, Peptidoglycan, Substrate Fragment, Carboxypeptidase, Cell Inner Membrane, Cell Membrane, Cell Shape, Cell Wall Biogenesis/Degradation, Hydrolase, Membrane, Peptidoglycan Synthesis, Protease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Chen, W. Zhang, Q. Shi, D. Hesek, M. Lee, S. Mobashery, B. K. Shoichet
Crystal Structures Of Penicillin-Binding Protein 6 From Escherichia Coli.
J. Am. Chem. Soc. V. 131 14345 2009
PubMed-ID: 19807181 | Reference-DOI: 10.1021/JA903773F

Molecule 1 - D-ALANYL-D-ALANINE CARBOXYPEPTIDASE DACC
	Chains	:	A, B, C, D
	EC Number	:	3.4.16.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-24A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	B0839, DACC, JW0823
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	DD-CARBOXYPEPTIDASE, DD-PEPTIDASE, PENICILLIN-BINDING PROTEIN 6, PBP-6

Molecule 2 - PEPTIDOGLYCAN SUBSTRATE (AMV)A(FGA)K(DAL)(DAL)
	Chains	:	L
	Engineered	:	YES
	Synthetic	:	YES

		1	2	3	4	5
Asymmetric Unit	:	A	B	C	D	L
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C		L
Biological Unit 4 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 11)

No.	Name	Count	Type	Full Name
1	AMV	1	Mod. Amino Acid	METHYL 2-(ACETYLAMINO)-3-O-[(1R)-1-CARBOXYETHYL]-2-DEOXY-BETA-D-GLUCOPYRANOSIDE
2	DAL	2	Mod. Amino Acid	D-ALANINE
3	FGA	1	Mod. Amino Acid	GAMMA-D-GLUTAMIC ACID
4	SO4	6	Ligand/Ion	SULFATE ION
5	SUC	1	Ligand/Ion	SUCROSE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	AMV	-1	Mod. Amino Acid	METHYL 2-(ACETYLAMINO)-3-O-[(1R)-1-CARBOXYETHYL]-2-DEOXY-BETA-D-GLUCOPYRANOSIDE
2	DAL	-1	Mod. Amino Acid	D-ALANINE
3	FGA	-1	Mod. Amino Acid	GAMMA-D-GLUTAMIC ACID
4	SO4	1	Ligand/Ion	SULFATE ION
5	SUC	-1	Ligand/Ion	SUCROSE

Biological Unit 2 (1, 3)

No.	Name	Count	Type	Full Name
1	AMV	-1	Mod. Amino Acid	METHYL 2-(ACETYLAMINO)-3-O-[(1R)-1-CARBOXYETHYL]-2-DEOXY-BETA-D-GLUCOPYRANOSIDE
2	DAL	-1	Mod. Amino Acid	D-ALANINE
3	FGA	-1	Mod. Amino Acid	GAMMA-D-GLUTAMIC ACID
4	SO4	3	Ligand/Ion	SULFATE ION
5	SUC	-1	Ligand/Ion	SUCROSE

Biological Unit 3 (5, 6)

No.	Name	Count	Type	Full Name
1	AMV	1	Mod. Amino Acid	METHYL 2-(ACETYLAMINO)-3-O-[(1R)-1-CARBOXYETHYL]-2-DEOXY-BETA-D-GLUCOPYRANOSIDE
2	DAL	2	Mod. Amino Acid	D-ALANINE
3	FGA	1	Mod. Amino Acid	GAMMA-D-GLUTAMIC ACID
4	SO4	1	Ligand/Ion	SULFATE ION
5	SUC	1	Ligand/Ion	SUCROSE

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	AMV	-1	Mod. Amino Acid	METHYL 2-(ACETYLAMINO)-3-O-[(1R)-1-CARBOXYETHYL]-2-DEOXY-BETA-D-GLUCOPYRANOSIDE
2	DAL	-1	Mod. Amino Acid	D-ALANINE
3	FGA	-1	Mod. Amino Acid	GAMMA-D-GLUTAMIC ACID
4	SO4	1	Ligand/Ion	SULFATE ION
5	SUC	-1	Ligand/Ion	SUCROSE

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:194 , THR A:210 , GLY A:211 , THR A:212 , ARG A:244 , HOH A:428 , HOH A:606	BINDING SITE FOR RESIDUE SO4 A 353
2	AC2	SOFTWARE	ARG A:190 , ARG B:194 , THR B:210 , GLY B:211 , THR B:212 , ARG B:244	BINDING SITE FOR RESIDUE SO4 B 353
3	AC3	SOFTWARE	HOH A:748 , ARG B:196 , ARG B:242	BINDING SITE FOR RESIDUE SO4 B 354
4	AC4	SOFTWARE	ARG A:242 , GLU B:183 , ARG B:190 , HOH B:421 , HOH B:689	BINDING SITE FOR RESIDUE SO4 B 355
5	AC5	SOFTWARE	THR C:240 , ARG C:242 , HOH C:383 , HOH C:490 , HOH C:652 , HOH C:782 , TRP D:199	BINDING SITE FOR RESIDUE SO4 C 353
6	AC6	SOFTWARE	ALA A:96 , ASP A:97 , LYS A:100 , HOH A:367 , HOH A:402 , LYS C:58 , HOH C:426	BINDING SITE FOR RESIDUE SUC C 354
7	AC7	SOFTWARE	ARG D:194 , THR D:210 , GLY D:211 , THR D:212 , ARG D:244 , HOH D:371	BINDING SITE FOR RESIDUE SO4 D 353

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

Asymmetric Unit

No.	Residues
1	Gly A:207	-	Met A:208
2	Ala A:317	-	Pro A:318
3	Gly B:207	-	Met B:208
4	Ala B:317	-	Pro B:318
5	Gly C:207	-	Met C:208
6	Ala C:317	-	Pro C:318
7	Gly C:351	-	Gly C:352
8	Gly D:207	-	Met D:208
9	Ala D:317	-	Pro D:318

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

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

(no "Exon" information available for 3ITB)

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:345
 aligned with DACC_ECOLI | P08506 from UniProtKB/Swiss-Prot  Length:400

    Alignment length:348
                                    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        
           DACC_ECOLI    31 TVEAPSVDARAWILMDYASGKVLAEGNADEKLDPASLTKIMTSYVVGQALKADKIKLTDMVTVGKDAWATGNPALRGSSVMFLKPGDQVSVADLNKGVIIQSGNDACIALADYVAGSQESFIGLMNGYAKKLGLTNTTFQTVHGLDAPGQFSTARDMALLGKALIHDVPEEYAIHKEKEFTFNKIRQPNRNRLLWSSNLNVDGMKTGTTAGAGYNLVASATQGDMRLISVVLGAKTDRIRFNESEKLLTWGFRFFETVTPIKPDATFVTQRVWFGDKSEVNLGAGEAGSVTIPRGQLKNLKASYTLTEPQLTAPLKKGQVVGTIDFQLNGKSIEQRPLIVMENVEEGG 378
               SCOP domains d3itba1 A:5-258 automated matches                                                                                                                                                                                                                             d3itba2 A:259-352 automated matches                                                            SCOP domains
               CATH domains 3itbA01 A:5-258 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                       3itbA02 A:259-350 Peptidoglycan synthesis regulatory factor (PBP3), Domain    2             -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........eeeeee.....eeeee.......hhhhhhhhhhhhhhhhhhh.......eee.hhhhh...hhhhh...........eeehhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhhhhhhh...eeee..eeee..hhhhhh...eeeeeeeee.....eeeeeeeee..eeeeeeeeee.hhhhhhhhhhhhhhhhhhheeee.........eeeeee.....eeeee......eeee......eeeeeee....ee.......eeeeeeeee.---.eeeeeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3itb A   5 TVEAPSVDARAWILMDYASGKVLAEGNADEKLDPASLTKIMTSYVVGQALKADKIKLTDMVTVGKDAWATGNPALRGSSVMFLKPGDQVSVADLNKGVIIQSGNDACIALADYVAGSQESFIGLMNGYAKKLGLTNTTFQTVHGLDAPGQFSTARDMALLGKALIHDVPEEYAIHKEKEFTFNKIRQPNRNRLLWSSNLNVDGMKTGTTAGAGYNLVASATQGDMRLISVVLGAKTDRIRFNESEKLLTWGFRFFETVTPIKPDATFVTQRVWFGDKSEVNLGAGEAGSVTIPRGQLKNLKASYTLTEPQLTAPLKKGQVVGTIDFQLN---IEQRPLIVMENVEEGG 352
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324        |-  |    344        
                                                                                                                                                                                                                                                                                                                                                                  333 337

Chain B from PDB  Type:PROTEIN  Length:346
 aligned with DACC_ECOLI | P08506 from UniProtKB/Swiss-Prot  Length:400

    Alignment length:346
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372      
           DACC_ECOLI    33 EAPSVDARAWILMDYASGKVLAEGNADEKLDPASLTKIMTSYVVGQALKADKIKLTDMVTVGKDAWATGNPALRGSSVMFLKPGDQVSVADLNKGVIIQSGNDACIALADYVAGSQESFIGLMNGYAKKLGLTNTTFQTVHGLDAPGQFSTARDMALLGKALIHDVPEEYAIHKEKEFTFNKIRQPNRNRLLWSSNLNVDGMKTGTTAGAGYNLVASATQGDMRLISVVLGAKTDRIRFNESEKLLTWGFRFFETVTPIKPDATFVTQRVWFGDKSEVNLGAGEAGSVTIPRGQLKNLKASYTLTEPQLTAPLKKGQVVGTIDFQLNGKSIEQRPLIVMENVEEGG 378
               SCOP domains d3itbb1 B:7-258 automated matches                                                                                                                                                                                                                           d3itbb2 B:259-352 automated matches                                                            SCOP domains
               CATH domains 3itbB01 B:7-258 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                     3itbB02 B:259-350 Peptidoglycan synthesis regulatory factor (PBP3), Domain 2                -- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeee.....eeeee.......hhhhhhhhhhhhhhhhhhh.......eee.hhhhh...hhhhh...........eeehhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhhhhh...eeee..eeee..hhhhhh...eeeeeeeee.....eeeeeeeee..eeeeeeeeee.hhhhhhhhhhhhhhhhhhheeee.........eeeeee.....eeeee......eeee..hhhhheeeeee....ee.......eeeeeeeee..eeeeeeeeee........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3itb B   7 EAPSVDARAWILMDYASGKVLAEGNADEKLDPASLTKIMTSYVVGQALKADKIKLTDMVTVGKDAWATGNPALRGSSVMFLKPGDQVSVADLNKGVIIQSGNDACIALADYVAGSQESFIGLMNGYAKKLGLTNTTFQTVHGLDAPGQFSTARDMALLGKALIHDVPEEYAIHKEKEFTFNKIRQPNRNRLLWSSNLNVDGMKTGTTAGAGYNLVASATQGDMRLISVVLGAKTDRIRFNESEKLLTWGFRFFETVTPIKPDATFVTQRVWFGDKSEVNLGAGEAGSVTIPRGQLKNLKASYTLTEPQLTAPLKKGQVVGTIDFQLNGKSIEQRPLIVMENVEEGG 352
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346

Chain C from PDB  Type:PROTEIN  Length:347
 aligned with DACC_ECOLI | P08506 from UniProtKB/Swiss-Prot  Length:400

    Alignment length:347
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       
           DACC_ECOLI    32 VEAPSVDARAWILMDYASGKVLAEGNADEKLDPASLTKIMTSYVVGQALKADKIKLTDMVTVGKDAWATGNPALRGSSVMFLKPGDQVSVADLNKGVIIQSGNDACIALADYVAGSQESFIGLMNGYAKKLGLTNTTFQTVHGLDAPGQFSTARDMALLGKALIHDVPEEYAIHKEKEFTFNKIRQPNRNRLLWSSNLNVDGMKTGTTAGAGYNLVASATQGDMRLISVVLGAKTDRIRFNESEKLLTWGFRFFETVTPIKPDATFVTQRVWFGDKSEVNLGAGEAGSVTIPRGQLKNLKASYTLTEPQLTAPLKKGQVVGTIDFQLNGKSIEQRPLIVMENVEEGG 378
               SCOP domains d3itbc1 C:6-258 automated matches                                                                                                                                                                                                                            d3itbc2 C:259-352 automated matches                                                            SCOP domains
               CATH domains 3itbC01 C:6-258 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                      3itbC02 C:259-350 Peptidoglycan synthesis regulatory factor (PBP3), Domain 2                -- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeee.....eeeee.......hhhhhhhhhhhhhhhhhhh.......eee.hhhhh...hhhhh...........eeehhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhhhhhhhhh.eeee..eeee..hhhhhh...eeeeeeeee.....eeeeeeeee..eeeeeeeeee.hhhhhhhhhhhhhhhhhhheeee.........eeeeee.....eeeeehhhhh.eeee..hhhhheeeeee....ee.......eeeeeeeee..eeeeeeeeee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3itb C   6 VEAPSVDARAWILMDYASGKVLAEGNADEKLDPASLTKIMTSYVVGQALKADKIKLTDMVTVGKDAWATGNPALRGSSVMFLKPGDQVSVADLNKGVIIQSGNDACIALADYVAGSQESFIGLMNGYAKKLGLTNTTFQTVHGLDAPGQFSTARDMALLGKALIHDVPEEYAIHKEKEFTFNKIRQPNRNRLLWSSNLNVDGMKTGTTAGAGYNLVASATQGDMRLISVVLGAKTDRIRFNESEKLLTWGFRFFETVTPIKPDATFVTQRVWFGDKSEVNLGAGEAGSVTIPRGQLKNLKASYTLTEPQLTAPLKKGQVVGTIDFQLNGKSIEQRPLIVMENVEEGG 352
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345

Chain D from PDB  Type:PROTEIN  Length:351
 aligned with DACC_ECOLI | P08506 from UniProtKB/Swiss-Prot  Length:400

    Alignment length:351
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377 
           DACC_ECOLI    28 AEQTVEAPSVDARAWILMDYASGKVLAEGNADEKLDPASLTKIMTSYVVGQALKADKIKLTDMVTVGKDAWATGNPALRGSSVMFLKPGDQVSVADLNKGVIIQSGNDACIALADYVAGSQESFIGLMNGYAKKLGLTNTTFQTVHGLDAPGQFSTARDMALLGKALIHDVPEEYAIHKEKEFTFNKIRQPNRNRLLWSSNLNVDGMKTGTTAGAGYNLVASATQGDMRLISVVLGAKTDRIRFNESEKLLTWGFRFFETVTPIKPDATFVTQRVWFGDKSEVNLGAGEAGSVTIPRGQLKNLKASYTLTEPQLTAPLKKGQVVGTIDFQLNGKSIEQRPLIVMENVEEGG 378
               SCOP domains d3itbd1 D:2-258 automated matches                                                                                                                                                                                                                                d3itbd2 D:259-352 automated matches                                                            SCOP domains
               CATH domains 3itbD01 D:2-258 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                          3itbD02 D:259-350 Peptidoglycan synthesis regulatory factor (PBP3), Domain 2                -- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeee.....eeeee.......hhhhhhhhhhhhhhhhhhh.......eee.hhhhh...hhhhh...........eeehhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhhhhh...eeee..eeee..hhhhhh...eeeeeeeee.....eeeeeeeee..eeeeeeeeee.hhhhhhhhhhhhhhhhhhheeee.........eeeeee.....eeeeehhhhh.eeee..hhh.eeeeeee....ee.......eeeeeeeee..eeeeeeeeee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3itb D   2 AEQTVEAPSVDARAWILMDYASGKVLAEGNADEKLDPASLTKIMTSYVVGQALKADKIKLTDMVTVGKDAWATGNPALRGSSVMFLKPGDQVSVADLNKGVIIQSGNDACIALADYVAGSQESFIGLMNGYAKKLGLTNTTFQTVHGLDAPGQFSTARDMALLGKALIHDVPEEYAIHKEKEFTFNKIRQPNRNRLLWSSNLNVDGMKTGTTAGAGYNLVASATQGDMRLISVVLGAKTDRIRFNESEKLLTWGFRFFETVTPIKPDATFVTQRVWFGDKSEVNLGAGEAGSVTIPRGQLKNLKASYTLTEPQLTAPLKKGQVVGTIDFQLNGKSIEQRPLIVMENVEEGG 352
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351

Chain L from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 3itb L 501 xAxKxx 506
                            | | ||
                          501-AMV|
                            503-FGA
                              505-DAL
                               506-DAL

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: All beta proteins (24004)

Fold: Penicillin-binding protein associated domain (19)

Superfamily: Penicillin-binding protein associated domain (19)

Family: automated matches (4)

Protein domain: automated matches (4)

Escherichia coli [TaxId: 562] (3)

1a	d3itba2	A:259-352
1b	d3itbb2	B:259-352
1c	d3itbc2	C:259-352
1d	d3itbd2	D:259-352

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

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

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

Family: automated matches (70)

Protein domain: automated matches (70)

Escherichia coli [TaxId: 562] (4)

2a	d3itba1	A:5-258
2b	d3itbb1	B:7-258
2c	d3itbc1	C:6-258
2d	d3itbd1	D:2-258

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)

Escherichia coli. Organism_taxid: 562. (91)

1a	3itbD01	D:2-258
1b	3itbA01	A:5-258
1c	3itbC01	C:6-258
1d	3itbB01	B:7-258

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Peptidoglycan synthesis regulatory factor (PBP3), Domain 2 (13)

Homologous Superfamily: Peptidoglycan synthesis regulatory factor (PBP3), Domain 2 (13)

Escherichia coli. Organism_taxid: 562. (9)

2a	3itbB02	B:259-350
2b	3itbC02	C:259-350
2c	3itbD02	D:259-350
2d	3itbA02	A:259-350

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (DACC_ECOLI | P08506)

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:0004175	endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain.
	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:0008658	penicillin binding	Interacting selectively and non-covalently with penicillin, any antibiotic that contains the condensed beta-lactamthiazolidine ring system.
	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.
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:0042493	response to drug	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 a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
cellular component
	GO:0005887	integral component of plasma membrane	The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric Unit
	Complete Structure
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	Ligands, Modified Residues, Ions
		AMV	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		DAL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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		SUC	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ala A:317 - Pro A:318	[ RasMol ]
		Ala B:317 - Pro B:318	[ RasMol ]
		Ala C:317 - Pro C:318	[ RasMol ]
		Ala D:317 - Pro D:318	[ RasMol ]
		Gly A:207 - Met A:208	[ RasMol ]
		Gly B:207 - Met B:208	[ RasMol ]
		Gly C:207 - Met C:208	[ RasMol ]
		Gly C:351 - Gly C:352	[ RasMol ]
		Gly D:207 - Met D:208	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]
		Biological Unit 4	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format \| Biol. Unit 3 PNG format \| Biol. Unit 4 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	3itb
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	DACC_ECOLI \| P08506
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	3.4.16.4
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

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		Disease Information	:	OMIM

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		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
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Access by UniProt ID/Accession number
	DACC_ECOLI \| P08506
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	DACC_ECOLI \| P08506	:	3it9 3ita

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 11)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (9, 9)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 8)

CATH Domains (2, 8)

Pfam Domains (0, 0)

Gene Ontology (14, 14)

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Databases

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File