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Title :   CRYSTAL STRUCTURE OF PENICILLIN-BINDING PROTEIN 3 FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH (5S)-PENICILLOIC ACID

Authors :   J. E. Nettleship, D. I. Stuart, R. J. Owens, J. Ren

Date :   15 May 13 (Deposition) - 06 Nov 13 (Release) - 06 Nov 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.01

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Penicillin-Binding Proteins, Piperacillin, (5S)-Penicilloic Acid, Cell Wall Biosynthesis, Transpeptidase, Out Periplasmic Membrane, Biosynthetic Protein, Biosynthetic Protein-Antibiotic Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. S. Van Berkel, J. E. Nettleship, I. K. Leung, J. Brem, H. Choi, D. I. Stuart, T. D. Claridge, M. A. Mcdonough, R. J. Owens, J. Ren, C. J. Schofield
Binding Of (5S)-Penicilloic Acid To Penicillin Binding Protein 3.
Acs Chem. Biol. V. 8 2112 2013
PubMed-ID: 23899657 | Reference-DOI: 10.1021/CB400200H

Molecule 1 - PENICILLIN-BINDING PROTEIN 3
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	FTSI, PA4418
	Organism Scientific	:	PSEUDOMONAS AERUGINOSA
	Organism Taxid	:	208964
	Strain	:	PAO1

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 19)

No.	Name	Count	Type	Full Name
1	CL	5	Ligand/Ion	CHLORIDE ION
2	GOL	9	Ligand/Ion	GLYCEROL
3	IMD	3	Ligand/Ion	IMIDAZOLE
4	VPP	2	Ligand/Ion	(2S,4S)-2-[(R)-CARBOXY{[(2R)-2-{[(4-ETHYL-2,3-DIOXOPIPERAZIN-1-YL)CARBONYL]AMINO}-2-PHENYLACETYL]AMINO}METHYL]-5,5-DIMETHYL-1,3-THIAZOLIDINE-4-CARBOXYLIC ACID

Biological Unit 1 (3, 8)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	5	Ligand/Ion	GLYCEROL
3	IMD	2	Ligand/Ion	IMIDAZOLE
4	VPP	1	Ligand/Ion	(2S,4S)-2-[(R)-CARBOXY{[(2R)-2-{[(4-ETHYL-2,3-DIOXOPIPERAZIN-1-YL)CARBONYL]AMINO}-2-PHENYLACETYL]AMINO}METHYL]-5,5-DIMETHYL-1,3-THIAZOLIDINE-4-CARBOXYLIC ACID

Biological Unit 2 (3, 6)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	4	Ligand/Ion	GLYCEROL
3	IMD	1	Ligand/Ion	IMIDAZOLE
4	VPP	1	Ligand/Ion	(2S,4S)-2-[(R)-CARBOXY{[(2R)-2-{[(4-ETHYL-2,3-DIOXOPIPERAZIN-1-YL)CARBONYL]AMINO}-2-PHENYLACETYL]AMINO}METHYL]-5,5-DIMETHYL-1,3-THIAZOLIDINE-4-CARBOXYLIC ACID

Asymmetric Unit (18, 18)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	SER A:294 , SER A:349 , ASN A:351 , TYR A:407 , TYR A:409 , SER A:485 , GLY A:486 , THR A:487 , ARG A:489 , TYR A:498 , TYR A:503 , PHE A:533 , GLY A:534 , GLY A:535 , IMD A:609 , HOH A:711 , HOH A:749 , HOH A:771 , HOH A:840	BINDING SITE FOR RESIDUE VPP A 601
02	AC2	SOFTWARE	ARG A:499 , ASN A:501	BINDING SITE FOR RESIDUE CL A 602
03	AC3	SOFTWARE	VAL A:493 , GLY A:494 , ARG B:233	BINDING SITE FOR RESIDUE CL A 603
04	AC4	SOFTWARE	GLY A:247 , SER A:248 , ARG A:284 , PHE A:290 , VAL A:523 , ASP A:525 , HOH A:705 , HOH A:805	BINDING SITE FOR RESIDUE GOL A 604
05	AC5	SOFTWARE	TYR A:268 , ASN A:269 , ASN A:272 , ARG A:273	BINDING SITE FOR RESIDUE GOL A 605
06	AC6	SOFTWARE	ASP A:428 , SER A:455 , GLN A:458 , HOH A:873	BINDING SITE FOR RESIDUE GOL A 606
07	AC7	SOFTWARE	ASN A:501 , PRO A:527 , SER A:528 , GLY A:531 , TYR A:532	BINDING SITE FOR RESIDUE GOL A 607
08	AC8	SOFTWARE	ARG A:473 , ALA A:530 , LEU A:536 , HOH A:763 , HOH A:804 , GLU B:176	BINDING SITE FOR RESIDUE GOL A 608
09	AC9	SOFTWARE	THR A:329 , THR A:404 , TYR A:407 , VPP A:601	BINDING SITE FOR RESIDUE IMD A 609
10	BC1	SOFTWARE	SER B:294 , LYS B:297 , SER B:349 , ASN B:351 , THR B:404 , TYR B:407 , TYR B:409 , SER B:485 , GLY B:486 , THR B:487 , ARG B:489 , TYR B:498 , TYR B:503 , PHE B:533 , GLY B:534 , GLY B:535 , IMD B:609 , HOH B:739 , HOH B:819 , HOH B:871 , HOH B:951	BINDING SITE FOR RESIDUE VPP B 601
11	BC2	SOFTWARE	VAL B:491 , ARG B:504	BINDING SITE FOR RESIDUE CL B 602
12	BC3	SOFTWARE	ARG B:499 , ASN B:501	BINDING SITE FOR RESIDUE CL B 603
13	BC4	SOFTWARE	LEU A:230 , ARG A:233 , VAL B:493 , GLY B:494	BINDING SITE FOR RESIDUE CL B 604
14	BC5	SOFTWARE	GLY B:247 , SER B:248 , ARG B:284 , VAL B:523 , ASP B:525 , HOH B:702 , HOH B:775	BINDING SITE FOR RESIDUE GOL B 605
15	BC6	SOFTWARE	ALA B:181 , LEU B:381 , HOH B:824	BINDING SITE FOR RESIDUE GOL B 606
16	BC7	SOFTWARE	TYR B:268 , ASN B:269 , ASN B:272 , ARG B:273	BINDING SITE FOR RESIDUE GOL B 607
17	BC8	SOFTWARE	GLU B:241 , LEU B:536 , PRO B:540 , HOH B:734 , HOH B:754 , HOH B:947	BINDING SITE FOR RESIDUE GOL B 608
18	BC9	SOFTWARE	THR B:329 , THR B:404 , TYR B:407 , VPP B:601	BINDING SITE FOR RESIDUE IMD B 609

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

Asymmetric Unit

No.	Residues
1	Gln A:265	-	Pro A:266
2	Tyr A:319	-	Pro A:320
3	Ala A:511	-	Pro A:512
4	Gln B:265	-	Pro B:266
5	Tyr B:319	-	Pro B:320
6	Ala B:511	-	Pro B:512

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

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

(no "Exon" information available for 4KQR)

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:520
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d4kqra1 A:51-221 automated matches                                                                                                                                         d4kqra2 A:222-570 automated matches                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee......ee.....eeeeeeeeeeeeehhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.....eeeeeeehhhhhhhhhh.....eeeeeeeeee..hhhhhhhhhh.........hhhhhhhhhhhh...eeeeeee.....eeeeeeeee.......ee...hhhhhhhhhhhhhhhhhhhh..eeeeeeee.....eeeeeee...........hhhhhhhhhhhh...hhhhhhhhhhhhhhhh.......eee....eeee..eeee.......eeehhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh........................hhhhhhhhhh......hhhhhhhhhhhhhh..ee..............ee..hhhhhhhhhhhhhhhhhh...hhhhh......eeeeeeeeee......eeeeeeeeeeeeee......eeeeeeee.......hhhhhhhhhhhhhhhhhhhhh.....hhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kqr A  51 RSVRHIAIPAHRGLITDRNGEPLAVSTPVTTLWANPKELMTAKERWPQLAAALGQDTKLFADRIEQNAEREFIYLVRGLTPEQGEGVIALKVPGVYSIEEFRRFYPAGEVVAHAVGFTDVDDRGREGIELAFDEWLAGVPGKRQVLKDRRGRVIKDVQVTKNAKPGKTLALSIDLRLQYLAHRELRNALLENGAKAGSLVIMDVKTGEILAMTNQPTYNPNNRRNLQPAAMRNRAMIDVFEPGSTVKPFSMSAALASGRWKPSDIVDVYPGTLQIGRYTIRDVSRNSRQLDLTGILIKSSNVGISKIAFDIGAESIYSVMQQVGLGQDTGLGFPGERVGNLPNHRKWPKAETATLAYGYGLSVTAIQLAHAYAALANDGKSVPLSMTRVDRVPDGVQVISPEVASTVQGMLQQVVEAQGGVFRAQVPGYHAAGKSGTARKVSVGTKGYRENAYRSLFAGFAPATDPRIAMVVVIDEPSKAGYFGGLVSAPVFSKVMAGALRLMNVPPDNLPTATEQQQVN 570
                                    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       470       480       490       500       510       520       530       540       550       560       570

Chain B from PDB  Type:PROTEIN  Length:518
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains d4kqrb1 B:53-221 automated matches                                                                                                                                       d4kqrb2 B:222-570 automated matches                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......ee.....eeeeeeeeeeeeehhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.....eeeeeeehhhhhhhhhh.....eeeeeeeeee..hhhhhhhhhh.........hhhhhhhhhhhh...eeeeeee.....eeeeeeeee.......ee...hhhhhhhhhhhhhhhhhhhh..eeeeeeee.....eeeeeee...........hhhhhhhhhhhh...hhhhhhhhhhhhhhhh.......eee....eeee..eeee.......eeehhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh........................hhhhhhhhhh......hhhhhhhhhhhhhh..ee..............ee..hhhhhhhhhhhhhhhhhh...hhhhh......eeeeeeeeee......eeeeeeeeeeeeee......eeeeeeee.......hhhhhhhhhhhhhhhhhhhhh.....hhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kqr B  53 VRHIAIPAHRGLITDRNGEPLAVSTPVTTLWANPKELMTAKERWPQLAAALGQDTKLFADRIEQNAEREFIYLVRGLTPEQGEGVIALKVPGVYSIEEFRRFYPAGEVVAHAVGFTDVDDRGREGIELAFDEWLAGVPGKRQVLKDRRGRVIKDVQVTKNAKPGKTLALSIDLRLQYLAHRELRNALLENGAKAGSLVIMDVKTGEILAMTNQPTYNPNNRRNLQPAAMRNRAMIDVFEPGSTVKPFSMSAALASGRWKPSDIVDVYPGTLQIGRYTIRDVSRNSRQLDLTGILIKSSNVGISKIAFDIGAESIYSVMQQVGLGQDTGLGFPGERVGNLPNHRKWPKAETATLAYGYGLSVTAIQLAHAYAALANDGKSVPLSMTRVDRVPDGVQVISPEVASTVQGMLQQVVEAQGGVFRAQVPGYHAAGKSGTARKVSVGTKGYRENAYRSLFAGFAPATDPRIAMVVVIDEPSKAGYFGGLVSAPVFSKVMAGALRLMNVPPDNLPTATEQQQVN 570
                                    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       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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 "CATH Domain" information available for 4KQR)

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

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Cis Peptide Bonds
		Ala A:511 - Pro A:512	[ RasMol ]
		Ala B:511 - Pro B:512	[ RasMol ]
		Gln A:265 - Pro A:266	[ RasMol ]
		Gln B:265 - Pro B:266	[ RasMol ]
		Tyr A:319 - Pro A:320	[ RasMol ]
		Tyr B:319 - Pro B:320	[ RasMol ]

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	FTSI_PSEAE \| G3XD46	:	3pbn 3pbo 3pbq 3pbr 3pbs 3pbt 4kqo 4kqq

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 19)

Sites (18, 18)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

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