3PAE - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE K84D MUTANT OF OXA-24/40 IN COMPLEX WITH DORIPENEM

Authors :   R. A. Powers, D. A. Leonard, K. D. Schneider

Date :   19 Oct 10 (Deposition) - 19 Jan 11 (Release) - 05 Oct 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Hydrolase, Carbapenemase, Hydrolase-Antibiotic Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. D. Schneider, C. J. Ortega, N. A. Renck, R. A. Bonomo, R. A. Powers, D. A. Leonard
Structures Of The Class D Carbapenemase Oxa-24 From Acinetobacter Baumannii In Complex With Doripenem.
J. Mol. Biol. V. 406 583 2011
PubMed-ID: 21215758 | Reference-DOI: 10.1016/J.JMB.2010.12.042
(for further references see the PDB file header)

Molecule 1 - BETA-LACTAMASE
	Chains	:	A, B
	EC Number	:	3.5.2.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET24A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 32-275
	Gene	:	BLAOXA-33, BLA-OXA-40, BLAOXA-24, BLAOXA-40, OXA-24, OXA40
	Mutation	:	YES
	Organism Scientific	:	ACINETOBACTER BAUMANNII
	Organism Taxid	:	470
	Synonym	:	BETA-LACTAMASE OXA-33, BETALACTAMASE OXA24, CARBAPENEM- HYDROLYZING BETA-LACTAMASE OXA-40, CARBAPENEM-HYDROLYZING OXACILLINASE, CLASS D BETA-LACTAMASE OXA-40, OXA-24 CLASS D BETA- LACTAMASE, OXA40

		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 (2, 5)

No.	Name	Count	Type	Full Name
1	4J6	2	Ligand/Ion	(4R,5S)-5-[(2S,3R)-3-HYDROXY-1-OXOBUTAN-2-YL]-4-METHYL-3-({(3S,5S)-5-[(SULFAMOYLAMINO)METHYL]PYRROLIDIN-3-YL}SULFANYL)-4,5-DIHYDRO-1H-PYRROLE-2-CARBOXYLIC ACID
2	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	4J6	1	Ligand/Ion	(4R,5S)-5-[(2S,3R)-3-HYDROXY-1-OXOBUTAN-2-YL]-4-METHYL-3-({(3S,5S)-5-[(SULFAMOYLAMINO)METHYL]PYRROLIDIN-3-YL}SULFANYL)-4,5-DIHYDRO-1H-PYRROLE-2-CARBOXYLIC ACID
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	4J6	1	Ligand/Ion	(4R,5S)-5-[(2S,3R)-3-HYDROXY-1-OXOBUTAN-2-YL]-4-METHYL-3-({(3S,5S)-5-[(SULFAMOYLAMINO)METHYL]PYRROLIDIN-3-YL}SULFANYL)-4,5-DIHYDRO-1H-PYRROLE-2-CARBOXYLIC ACID
2	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:8 , ALA A:80 , SER A:81 , TRP A:115 , LEU A:127 , SER A:128 , LEU A:168 , SER A:219 , GLY A:220 , TRP A:221 , MET A:223 , GLY A:258 , SER A:259 , ARG A:261 , HOH A:284 , HOH A:390 , HOH A:392 , HOH A:406	BINDING SITE FOR RESIDUE 4J6 A 300
2	AC2	SOFTWARE	GLY A:141 , LEU A:142 , GLU A:143 , HOH A:288 , HOH A:364	BINDING SITE FOR RESIDUE SO4 A 1
3	AC3	SOFTWARE	ALA B:80 , SER B:81 , TRP B:115 , LEU B:127 , SER B:128 , VAL B:130 , LEU B:168 , SER B:219 , GLY B:220 , TRP B:221 , MET B:223 , GLY B:258 , SER B:259 , ARG B:261 , HOH B:314 , HOH B:351 , HOH B:355 , HOH B:401	BINDING SITE FOR RESIDUE 4J6 B 300
4	AC4	SOFTWARE	HOH A:356 , GLY B:141 , LEU B:142 , GLU B:143	BINDING SITE FOR RESIDUE SO4 B 2
5	AC5	SOFTWARE	GLU B:76 , TYR B:77 , VAL B:78 , VAL B:225 , PRO B:227 , VAL B:229 , HOH B:402	BINDING SITE FOR RESIDUE SO4 B 3

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

Asymmetric Unit

No.	Residues
1	Gly A:170	-	Pro A:171
2	Thr A:226	-	Pro A:227
3	Gly B:170	-	Pro B:171
4	Thr B:226	-	Pro B:227

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

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

(no "Exon" information available for 3PAE)

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:244
 aligned with Q8RLA6_ACIBA | Q8RLA6 from UniProtKB/TrEMBL  Length:275

    Alignment length:244
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271    
         Q8RLA6_ACIBA    32 HISSQQHEKAIKSYFDEAQTQGVIIIKEGKNLSTYGNALARANKEYVPASTFKMLNALIGLENHKATTNEIFKWDGKKRTYPMWEKDMTLGEAMALSAVPVYQELARRTGLELMQKEVKRVNFGNTNIGTQVDNFWLVGPLKITPVQEVNFADDLAHNRLPFKLETQEEVKKMLLIKEVNGSKIYAKSGWGMGVTPQVGWLTGWVEQANGKKIPFSLNLEMKEGMSGSIRNEITYKSLENLGII 275
               SCOP domains d3paea_ A: automated matches                                                                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh...eeeeeee..eeeeee.hhhhhhh...hhhhhhhhhhhhhhhh.................hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhhh.....hhhhhhhhhhh.eeeee..eeeeeeeeee.....eeeeeeeeee.....eeeeeeeeee.....hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pae A  32 HISSQQHEKAIKSYFDEAQTQGVIIIKEGKNLSTYGNALARANKEYVPASTFDMLNALIGLENHKATTNEIFKWDGKKRTYPMWEKDMTLGEAMALSAVPVYQELARRTGLELMQKEVKRVNFGNTNIGTQVDNFWLVGPLKITPVQEVNFADDLAHNRLPFKLETQEEVKKMLLIKEVNGSKIYAKSGWGMGVTPQVGWLTGWVEQANGKKIPFSLNLEMKEGMSGSIRNEITYKSLENLGII 275
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271

Chain B from PDB  Type:PROTEIN  Length:244
 aligned with Q8RLA6_ACIBA | Q8RLA6 from UniProtKB/TrEMBL  Length:275

    Alignment length:244
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271    
         Q8RLA6_ACIBA    32 HISSQQHEKAIKSYFDEAQTQGVIIIKEGKNLSTYGNALARANKEYVPASTFKMLNALIGLENHKATTNEIFKWDGKKRTYPMWEKDMTLGEAMALSAVPVYQELARRTGLELMQKEVKRVNFGNTNIGTQVDNFWLVGPLKITPVQEVNFADDLAHNRLPFKLETQEEVKKMLLIKEVNGSKIYAKSGWGMGVTPQVGWLTGWVEQANGKKIPFSLNLEMKEGMSGSIRNEITYKSLENLGII 275
               SCOP domains d3paeb_ B: automated matches                                                                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Transpeptidase-3paeB01 B:32-270                                                                                                                                                                                                                ----- Pfam domains (1)
           Pfam domains (2) Transpeptidase-3paeB02 B:32-270                                                                                                                                                                                                                ----- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhh...eeeeeee..eeeeee.hhhhhhh...hhhhhhhhhhhhhhhh.................hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhhh.....hhhhhhhhhhh.eeeee..eeeeeeeeee.....eeeeeeeeee.....eeeeeeeeee.....hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pae B  32 HISSQQHEKAIKSYFDEAQTQGVIIIKEGKNLSTYGNALARANKEYVPASTFDMLNALIGLENHKATTNEIFKWDGKKRTYPMWEKDMTLGEAMALSAVPVYQELARRTGLELMQKEVKRVNFGNTNIGTQVDNFWLVGPLKITPVQEVNFADDLAHNRLPFKLETQEEVKKMLLIKEVNGSKIYAKSGWGMGVTPQVGWLTGWVEQANGKKIPFSLNLEMKEGMSGSIRNEITYKSLENLGII 275
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

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

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

Family: automated matches (70)

Protein domain: automated matches (70)

Acinetobacter baumannii [TaxId: 470] (19)

1a	d3paea_	A:
1b	d3paeb_	B:

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Beta-lactamase (210)

Family: Transpeptidase (31)

Acinetobacter baumannii (3)

1a	Transpeptidase-3paeB01	B:32-270
1b	Transpeptidase-3paeB02	B:32-270

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q8RLA6_ACIBA | Q8RLA6)

molecular function
	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.

Asymmetric Unit
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	Cis Peptide Bonds
		Gly A:170 - Pro A:171	[ RasMol ]
		Gly B:170 - Pro B:171	[ RasMol ]
		Thr A:226 - Pro A:227	[ RasMol ]
		Thr B:226 - Pro B:227	[ RasMol ]

Biological Units
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	Q8RLA6_ACIBA \| Q8RLA6	:	5vfd
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	Q8RLA6_ACIBA \| Q8RLA6	:	2jc7 3fv7 3fyz 3fzc 3g4p 3mbz 3pag 3znt 4f94 4wm9 5tg4 5tg5 5tg6 5tg7

3isg	THE NON-CARBAPENEMASE OXA-1 IN COMPLEX WITH THE SAME DRUG, DORIPENEM.
3pag

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

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