3IT9 - 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 APO STATE

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) - 10 Nov 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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 :   Penicillin-Binding Protein, Pbp6, Dd-Carboxypeptidase, Peptidoglycan, 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
(for further references see the PDB file header)

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	:	DACC
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	DD-CARBOXYPEPTIDASE, DD-PEPTIDASE, PENICILLIN- BINDING PROTEIN 6, PBP-6

		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 (2, 10)

No.	Name	Count	Type	Full Name
1	SO4	8	Ligand/Ion	SULFATE ION
2	SUC	2	Ligand/Ion	SUCROSE

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	SO4	-1	Ligand/Ion	SULFATE ION
2	SUC	-1	Ligand/Ion	SUCROSE

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION
2	SUC	-1	Ligand/Ion	SUCROSE

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION
2	SUC	-1	Ligand/Ion	SUCROSE

Biological Unit 4 (1, 3)

No.	Name	Count	Type	Full Name
1	SO4	3	Ligand/Ion	SULFATE ION
2	SUC	-1	Ligand/Ion	SUCROSE

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:194 , THR A:210 , GLY A:211 , THR A:212 , ARG A:244 , HOH A:465	BINDING SITE FOR RESIDUE SO4 A 353
02	AC2	SOFTWARE	ARG A:242 , HOH A:437 , HOH A:464 , GLU B:183 , ARG B:190	BINDING SITE FOR RESIDUE SO4 A 354
03	AC3	SOFTWARE	ALA A:96 , ASP A:97 , LYS A:100 , HOH A:416 , HOH A:502 , ASP C:57 , LYS C:58	BINDING SITE FOR RESIDUE SUC A 355
04	AC4	SOFTWARE	ARG A:196 , LEU A:197 , TRP A:199 , SER A:200 , SER A:201 , ASN A:202 , GLU A:249 , ARG B:196 , TRP B:199 , SO4 B:354	BINDING SITE FOR RESIDUE SUC A 356
05	AC5	SOFTWARE	ARG A:190 , ARG B:194 , THR B:210 , GLY B:211 , THR B:212 , ARG B:244 , HOH B:435	BINDING SITE FOR RESIDUE SO4 B 353
06	AC6	SOFTWARE	ARG A:242 , SUC A:356 , GLU B:183 , TRP B:199	BINDING SITE FOR RESIDUE SO4 B 354
07	AC7	SOFTWARE	ARG C:194 , THR C:210 , GLY C:211 , THR C:212 , ARG C:244 , HOH C:390	BINDING SITE FOR RESIDUE SO4 C 353
08	AC8	SOFTWARE	SER D:40 , SER D:106 , THR D:210 , GLY D:211 , THR D:212 , HOH D:378 , HOH D:395 , HOH D:424	BINDING SITE FOR RESIDUE SO4 D 353
09	AC9	SOFTWARE	GLU C:183 , TRP C:199 , HOH C:358 , THR D:240 , ARG D:242	BINDING SITE FOR RESIDUE SO4 D 354
10	BC1	SOFTWARE	THR C:240 , ARG C:242 , TRP D:199	BINDING SITE FOR RESIDUE SO4 D 355

(no "SS Bond" information available for 3IT9)

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 B:334	-	Lys B:335
6	Gly C:207	-	Met C:208
7	Ala C:317	-	Pro C:318
8	Gly D:207	-	Met D:208
9	Ala D:317	-	Pro D:318
10	Gly D:351	-	Gly D:352

(no "SAP(SNP)/Variant" information available for 3IT9)

(no "PROSITE Motif" information available for 3IT9)

(no "Exon" information available for 3IT9)

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:348
 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 d3it9a1 A:5-258 automated matches                                                                                                                                                                                                                             d3it9a2 A:259-352 automated matches                                                            SCOP domains
               CATH domains 3it9A01 A:5-258 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                       3it9A02 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...................hhhhhhhhhhhhhhhhhhhhhhhhh.eeee..eeee..hhhhhh...eeeeeeeee.....eeeeeeeee..eeeeeeeeee.hhhhhhhhhhhhhhhhhhheeee.........eeeeee.....eeeee......eeee..hhh.eeeeeee....ee.......eeeeeeeee..eeeeeeeeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3it9 A   5 TVEAPSVDARAWILMDYASGKVLAEGNADEKLDPASLTKIMTSYVVGQALKADKIKLTDMVTVGKDAWATGNPALRGSSVMFLKPGDQVSVADLNKGVIIQSGNDACIALADYVAGSQESFIGLMNGYAKKLGLTNTTFQTVHGLDAPGQFSTARDMALLGKALIHDVPEEYAIHKEKEFTFNKIRQPNRNRLLWSSNLNVDGMKTGTTAGAGYNLVASATQGDMRLISVVLGAKTDRIRFNESEKLLTWGFRFFETVTPIKPDATFVTQRVWFGDKSEVNLGAGEAGSVTIPRGQLKNLKASYTLTEPQLTAPLKKGQVVGTIDFQLNGKSIEQRPLIVMENVEEGG 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       334       344

Chain B from PDB  Type:PROTEIN  Length:345
 aligned with DACC_ECOLI | P08506 from UniProtKB/Swiss-Prot  Length:400

    Alignment length:345
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373     
           DACC_ECOLI    34 APSVDARAWILMDYASGKVLAEGNADEKLDPASLTKIMTSYVVGQALKADKIKLTDMVTVGKDAWATGNPALRGSSVMFLKPGDQVSVADLNKGVIIQSGNDACIALADYVAGSQESFIGLMNGYAKKLGLTNTTFQTVHGLDAPGQFSTARDMALLGKALIHDVPEEYAIHKEKEFTFNKIRQPNRNRLLWSSNLNVDGMKTGTTAGAGYNLVASATQGDMRLISVVLGAKTDRIRFNESEKLLTWGFRFFETVTPIKPDATFVTQRVWFGDKSEVNLGAGEAGSVTIPRGQLKNLKASYTLTEPQLTAPLKKGQVVGTIDFQLNGKSIEQRPLIVMENVEEGG 378
               SCOP domains d3it9b1 B:8-258 automated matches                                                                                                                                                                                                                          d3it9b2 B:259-352 automated matches                                                            SCOP domains
               CATH domains 3it9B01 B:8-258 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                    3it9B02 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...........eeehhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhhhhhhh.eeee..eeee..hhhhhh...eeeeeeeee.....eeeeeeeee..eeeeeeeeee.hhhhhhhhhhhhhhhhhhheeee.........eeeeee.....eeeeehhhhh.eeee..hhhhheeeeee....ee.......eeeeeeee....eeeeeeeee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3it9 B   8 APSVDARAWILMDYASGKVLAEGNADEKLDPASLTKIMTSYVVGQALKADKIKLTDMVTVGKDAWATGNPALRGSSVMFLKPGDQVSVADLNKGVIIQSGNDACIALADYVAGSQESFIGLMNGYAKKLGLTNTTFQTVHGLDAPGQFSTARDMALLGKALIHDVPEEYAIHKEKEFTFNKIRQPNRNRLLWSSNLNVDGMKTGTTAGAGYNLVASATQGDMRLISVVLGAKTDRIRFNESEKLLTWGFRFFETVTPIKPDATFVTQRVWFGDKSEVNLGAGEAGSVTIPRGQLKNLKASYTLTEPQLTAPLKKGQVVGTIDFQLNGKSIEQRPLIVMENVEEGG 352
                                    17        27        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

Chain C from PDB  Type:PROTEIN  Length:345
 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 d3it9c1 C:7-258 automated matches                                                                                                                                                                                                                           d3it9c2 C:259-352 automated matches                                                            SCOP domains
               CATH domains 3it9C01 C:7-258 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                     3it9C02 C:259-350 Peptidoglycan synthesis regulatory factor (PBP3), Domain  2               -- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeee.....eeeee.......hhhhhhhhhhhhhhhhhhh.......eee.hhhhh...................eeehhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhhhhhhhhh.eeee..eeee..hhhhhh...eeeeeeeeee...eeeeeeeeee..eeeeeeeeee.hhhhhhhhhhhhhhhhhhheeee.........eeeeee.....eeeeehhhhh.eeee..hhhhheeeeee....ee.......eeeeeeee.-..eeeeeeeee........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3it9 C   7 EAPSVDARAWILMDYASGKVLAEGNADEKLDPASLTKIMTSYVVGQALKADKIKLTDMVTVGKDAWATGNPALRGSSVMFLKPGDQVSVADLNKGVIIQSGNDACIALADYVAGSQESFIGLMNGYAKKLGLTNTTFQTVHGLDAPGQFSTARDMALLGKALIHDVPEEYAIHKEKEFTFNKIRQPNRNRLLWSSNLNVDGMKTGTTAGAGYNLVASATQGDMRLISVVLGAKTDRIRFNESEKLLTWGFRFFETVTPIKPDATFVTQRVWFGDKSEVNLGAGEAGSVTIPRGQLKNLKASYTLTEPQLTAPLKKGQVVGTIDFQL-GKSIEQRPLIVMENVEEGG 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      
                                                                                                                                                                                                                                                                                                                                                               332 |                  
                                                                                                                                                                                                                                                                                                                                                                 334

Chain D from PDB  Type:PROTEIN  Length:350
 aligned with DACC_ECOLI | P08506 from UniProtKB/Swiss-Prot  Length:400

    Alignment length:350
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378
           DACC_ECOLI    29 EQTVEAPSVDARAWILMDYASGKVLAEGNADEKLDPASLTKIMTSYVVGQALKADKIKLTDMVTVGKDAWATGNPALRGSSVMFLKPGDQVSVADLNKGVIIQSGNDACIALADYVAGSQESFIGLMNGYAKKLGLTNTTFQTVHGLDAPGQFSTARDMALLGKALIHDVPEEYAIHKEKEFTFNKIRQPNRNRLLWSSNLNVDGMKTGTTAGAGYNLVASATQGDMRLISVVLGAKTDRIRFNESEKLLTWGFRFFETVTPIKPDATFVTQRVWFGDKSEVNLGAGEAGSVTIPRGQLKNLKASYTLTEPQLTAPLKKGQVVGTIDFQLNGKSIEQRPLIVMENVEEGG 378
               SCOP domains d3it9d1 D:3-258 automated matches                                                                                                                                                                                                                               d3it9d2 D:259-352 automated matches                                                            SCOP domains
               CATH domains 3it9D01 D:3-258 DD-peptidase/beta-lactamase superfamily                                                                                                                                                                                                         3it9D02 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..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhhhhhhhhh.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
                 3it9 D   3 EQTVEAPSVDARAWILMDYASGKVLAEGNADEKLDPASLTKIMTSYVVGQALKADKIKLTDMVTVGKDAWATGNPALRGSSVMFLKPGDQVSVADLNKGVIIQSGNDACIALADYVAGSQESFIGLMNGYAKKLGLTNTTFQTVHGLDAPGQFSTARDMALLGKALIHDVPEEYAIHKEKEFTFNKIRQPNRNRLLWSSNLNVDGMKTGTTAGAGYNLVASATQGDMRLISVVLGAKTDRIRFNESEKLLTWGFRFFETVTPIKPDATFVTQRVWFGDKSEVNLGAGEAGSVTIPRGQLKNLKASYTLTEPQLTAPLKKGQVVGTIDFQLNGKSIEQRPLIVMENVEEGG 352
                                    12        22        32        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

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	d3it9a2	A:259-352
1b	d3it9c2	C:259-352
1c	d3it9d2	D:259-352
1d	d3it9b2	B: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	d3it9a1	A:5-258
2b	d3it9b1	B:8-258
2c	d3it9c1	C:7-258
2d	d3it9d1	D:3-258

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	3it9D01	D:3-258
1b	3it9A01	A:5-258
1c	3it9C01	C:7-258
1d	3it9B01	B:8-258

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	3it9A02	A:259-350
2b	3it9B02	B:259-350
2c	3it9D02	D:259-350
2d	3it9C02	C:259-350

(no "Pfam Domain" information available for 3IT9)

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
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	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 B:334 - Lys B:335	[ RasMol ]
		Gly C:207 - Met C:208	[ RasMol ]
		Gly D:207 - Met D:208	[ RasMol ]
		Gly D:351 - Gly D:352	[ RasMol ]

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

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Access by PDB/NDB ID
	3it9
		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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	(no 'MIM ID' available)
		Disease Information	:	OMIM

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	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	DACC_ECOLI \| P08506
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 10)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (10, 10)

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)

Visualization

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Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File