4MLL - JenaLib

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Biological Unit 4 (Jmol Viewer)

Title :   THE 1.4 A STRUCTURE OF THE CLASS D BETA-LACTAMASE OXA-1 K70D COMPLEXED WITH OXACILLIN

Authors :   C. M. June, B. C. Vallier, R. A. Bonomo, D. A. Leonard, R. A. Powers

Date :   06 Sep 13 (Deposition) - 09 Oct 13 (Release) - 08 Jan 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.37

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

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

Reference :   C. M. June, B. C. Vallier, R. A. Bonomo, D. A. Leonard, R. A. Powers
Structural Origins Of Oxacillinase Specificity In Class D Beta-Lactamases.
Antimicrob. Agents Chemother. V. 58 333 2014
PubMed-ID: 24165180 | Reference-DOI: 10.1128/AAC.01483-13

Molecule 1 - BETA-LACTAMASE OXA-1
	Chains	:	A, B, C, D
	EC Number	:	3.5.2.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET24A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 26-276
	Gene	:	BLA, BLA OXA1, OXA1
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	PENICILLINASE

		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 (3, 14)

No.	Name	Count	Type	Full Name
1	1S6	4	Ligand/Ion	(2R,4S)-5,5-DIMETHYL-2-[(1R)-1-{[(5-METHYL-3-PHENYL-1,2-OXAZOL-4-YL)CARBONYL]AMINO}-2-OXOETHYL]-1,3-THIAZOLIDINE-4-CARBOXYLIC ACID
2	MPD	3	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	PO4	7	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (3, 5)

No.	Name	Count	Type	Full Name
1	1S6	1	Ligand/Ion	(2R,4S)-5,5-DIMETHYL-2-[(1R)-1-{[(5-METHYL-3-PHENYL-1,2-OXAZOL-4-YL)CARBONYL]AMINO}-2-OXOETHYL]-1,3-THIAZOLIDINE-4-CARBOXYLIC ACID
2	MPD	1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	PO4	3	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	1S6	1	Ligand/Ion	(2R,4S)-5,5-DIMETHYL-2-[(1R)-1-{[(5-METHYL-3-PHENYL-1,2-OXAZOL-4-YL)CARBONYL]AMINO}-2-OXOETHYL]-1,3-THIAZOLIDINE-4-CARBOXYLIC ACID
2	MPD	-1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 3 (2, 3)

No.	Name	Count	Type	Full Name
1	1S6	1	Ligand/Ion	(2R,4S)-5,5-DIMETHYL-2-[(1R)-1-{[(5-METHYL-3-PHENYL-1,2-OXAZOL-4-YL)CARBONYL]AMINO}-2-OXOETHYL]-1,3-THIAZOLIDINE-4-CARBOXYLIC ACID
2	MPD	-1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 4 (3, 4)

No.	Name	Count	Type	Full Name
1	1S6	1	Ligand/Ion	(2R,4S)-5,5-DIMETHYL-2-[(1R)-1-{[(5-METHYL-3-PHENYL-1,2-OXAZOL-4-YL)CARBONYL]AMINO}-2-OXOETHYL]-1,3-THIAZOLIDINE-4-CARBOXYLIC ACID
2	MPD	2	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
3	PO4	1	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:66 , SER A:67 , MET A:99 , TRP A:102 , SER A:115 , VAL A:117 , THR A:213 , GLY A:214 , ALA A:215 , LEU A:255 , SER A:258 , HOH A:458 , HOH A:477 , HOH A:502 , LYS B:236 , SER B:237 , GLY B:238	BINDING SITE FOR RESIDUE 1S6 A 301
02	AC2	SOFTWARE	GLU A:122 , HOH A:620	BINDING SITE FOR RESIDUE PO4 A 302
03	AC3	SOFTWARE	ASN A:193 , GLU A:196	BINDING SITE FOR RESIDUE PO4 A 303
04	AC4	SOFTWARE	ASN A:250 , GLY A:252 , ASN B:193 , GLU B:196	BINDING SITE FOR RESIDUE PO4 A 305
05	AC5	SOFTWARE	ASN A:130 , LYS A:133 , HOH A:632 , PHE C:114 , TYR C:199 , LEU C:200 , HOH C:476 , HOH C:511 , HOH C:624	BINDING SITE FOR RESIDUE MPD A 304
06	AC6	SOFTWARE	LYS A:236 , GLY A:238 , HOH A:505 , ASP B:66 , SER B:67 , MET B:99 , TRP B:102 , SER B:115 , VAL B:117 , GLY B:214 , ALA B:215 , LEU B:255 , SER B:258 , HOH B:414 , HOH B:424 , HOH B:450 , HOH B:452 , HOH B:494 , HOH B:587	BINDING SITE FOR RESIDUE 1S6 B 301
07	AC7	SOFTWARE	GLU B:122 , HOH B:545	BINDING SITE FOR RESIDUE PO4 B 302
08	AC8	SOFTWARE	ASP C:66 , SER C:67 , TRP C:102 , SER C:115 , VAL C:117 , THR C:213 , GLY C:214 , ALA C:215 , SER C:258 , HOH C:438 , HOH C:556 , HOH C:576 , HOH C:641 , LYS D:236 , GLY D:238	BINDING SITE FOR RESIDUE 1S6 C 301
09	AC9	SOFTWARE	ASN C:193 , GLU C:196 , ASN D:250 , LEU D:251 , GLY D:252	BINDING SITE FOR RESIDUE PO4 C 302
10	BC1	SOFTWARE	ILE C:82 , PHE C:90 , HOH D:576	BINDING SITE FOR RESIDUE PO4 C 303
11	BC2	SOFTWARE	LYS C:236 , SER C:237 , GLY C:238 , ASP D:66 , SER D:67 , MET D:99 , TRP D:102 , SER D:115 , VAL D:117 , THR D:213 , GLY D:214 , ALA D:215 , LEU D:255 , SER D:258 , HOH D:415 , HOH D:478 , HOH D:490	BINDING SITE FOR RESIDUE 1S6 D 301
12	BC3	SOFTWARE	GLU D:122 , LYS D:126 , HOH D:532	BINDING SITE FOR RESIDUE PO4 D 302
13	BC4	SOFTWARE	GLN B:113 , TYR B:199 , LEU B:200 , HOH B:500 , HOH B:569 , HOH B:591 , LYS D:133	BINDING SITE FOR RESIDUE MPD D 303
14	BC5	SOFTWARE	LEU C:251 , GLY C:252 , GLU D:192 , ASN D:193 , GLU D:196 , HOH D:619	BINDING SITE FOR RESIDUE MPD D 304

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

(no "Cis Peptide Bond" information available for 4MLL)

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

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

(no "Exon" information available for 4MLL)

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
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Chain A from PDB  Type:PROTEIN  Length:250
                                                                                                                                                                                                                                                                                          
               SCOP domains d4mlla_ A: Class D beta-lactamase                                                                                                                                                                                                                          SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh..eeeeeeee.....eeeeehhhhhh....hhhhhhhhhhhhhhhh.................hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhh........hhhhhhhhhhhhhh.....hhhhhhhhhhhheeee.....eeeeeeeeee......eeeeeeeeee.....eeeeeeeeee......hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mll A  19 TDISTVASPLFEGTEGCFLLYDASTNAEIAQFNKAKCATQMAPDSTFDIALSLMAFDAEIIDQKTIFKWDKTPKGMEIWNSNHTPKTWMQFSVVWVSQEITQKIGLNKIKNYLKDFDYGNQDFSGDKERNNGLTEAWLESSLKISPEEQIQFLRKIINHNLPVKNSAIENTIENMYLQDLDNSTKLYGKTGAGFTANRTLQNGWFEGFIISKSGHKYVFVSALTGNLGSNLTSSIKAKKNAITILNTLNL 274
                                    28 ||     40  ||    52        62        72        82||      93       103       113       123       133       143       153       163       173       183       193       203       213   ||  224       234       244       254       264       274
                                      30|        43|                                   83|                                                                                                                                 217|                                                       
                                       33         46                                    85                                                                                                                                  219

Chain B from PDB  Type:PROTEIN  Length:251
                                                                                                                                                                                                                                                                                           
               SCOP domains d4mllb_ B: Class D beta-lactamase                                                                                                                                                                                                                           SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhhhhhhh..eeeeeeee.....eeeeehhhhhh....hhhhhhhhhhhhhhhh.................hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhh........hhhhhhhhhhhhhh.....hhhhhhhhhhhheeee.....eeeeeeeeee......eeeeeeeeee.....eeeeeeeeee......hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mll B  18 STDISTVASPLFEGTEGCFLLYDASTNAEIAQFNKAKCATQMAPDSTFDIALSLMAFDAEIIDQKTIFKWDKTPKGMEIWNSNHTPKTWMQFSVVWVSQEITQKIGLNKIKNYLKDFDYGNQDFSGDKERNNGLTEAWLESSLKISPEEQIQFLRKIINHNLPVKNSAIENTIENMYLQDLDNSTKLYGKTGAGFTANRTLQNGWFEGFIISKSGHKYVFVSALTGNLGSNLTSSIKAKKNAITILNTLNL 274
                                    27  ||    39   ||   51        61        71        81 ||     92       102       112       122       132       142       152       162       172       182       192       202       212    || 223       233       243       253       263       273 
                                       30|        43|                                   83|                                                                                                                                 217|                                                       
                                        33         46                                    85                                                                                                                                  219

Chain C from PDB  Type:PROTEIN  Length:251
                                                                                                                                                                                                                                                                                           
               SCOP domains d4mllc_ C: Class D beta-lactamase                                                                                                                                                                                                                           SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eehhhhhhhhhh.eeeeeeeee.....eeeeehhhhhh....hhhhhhhhhhhhhhhh.................hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhh........hhhhhhhhhhhhhh.....hhhhhhhhhhhheeee.....eeeeeeeeee......eeeeeeeeee.....eeeeeeeeee......hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mll C  18 STDISTVASPLFEGTEGCFLLYDASTNAEIAQFNKAKCATQMAPDSTFDIALSLMAFDAEIIDQKTIFKWDKTPKGMEIWNSNHTPKTWMQFSVVWVSQEITQKIGLNKIKNYLKDFDYGNQDFSGDKERNNGLTEAWLESSLKISPEEQIQFLRKIINHNLPVKNSAIENTIENMYLQDLDNSTKLYGKTGAGFTANRTLQNGWFEGFIISKSGHKYVFVSALTGNLGSNLTSSIKAKKNAITILNTLNL 274
                                    27  ||    39   ||   51        61        71        81 ||     92       102       112       122       132       142       152       162       172       182       192       202       212    || 223       233       243       253       263       273 
                                       30|        43|                                   83|                                                                                                                                 217|                                                       
                                        33         46                                    85                                                                                                                                  219

Chain D from PDB  Type:PROTEIN  Length:250
                                                                                                                                                                                                                                                                                          
               SCOP domains d4mlld_ D: Class D beta-lactamase                                                                                                                                                                                                                          SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh..eeeeeeee.....eeeeehhhhhh....hhhhhhhhhhhhhhhh.................hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhh........hhhhhhhhhhhhhh.....hhhhhhhhhhhheeee.....eeeeeeeeee......eeeeeeeeee.....eeeeeeeeee......hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mll D  19 TDISTVASPLFEGTEGCFLLYDASTNAEIAQFNKAKCATQMAPDSTFDIALSLMAFDAEIIDQKTIFKWDKTPKGMEIWNSNHTPKTWMQFSVVWVSQEITQKIGLNKIKNYLKDFDYGNQDFSGDKERNNGLTEAWLESSLKISPEEQIQFLRKIINHNLPVKNSAIENTIENMYLQDLDNSTKLYGKTGAGFTANRTLQNGWFEGFIISKSGHKYVFVSALTGNLGSNLTSSIKAKKNAITILNTLNL 274
                                    28 ||     40  ||    52        62        72        82||      93       103       113       123       133       143       153       163       173       183       193       203       213   ||  224       234       244       254       264       274
                                      30|        43|                                   83|                                                                                                                                 217|                                                       
                                       33         46                                    85                                                                                                                                  219

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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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

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

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

Family: beta-Lactamase/D-ala carboxypeptidase (411)

Protein domain: Class D beta-lactamase (32)

Escherichia coli, OXA-1 [TaxId: 562] (3)

1a	d4mlla_	A:
1b	d4mllb_	B:
1c	d4mllc_	C:
1d	d4mlld_	D:

(no "CATH Domain" information available for 4MLL)

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

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4f94	STRUCTURE OF THE CLASS D BETA-LACTAMASE OXA-24 K84D IN ACYL -ENZYME COMPLEX WITH OXACILLIN

Description

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Ligands, Modified Residues, Ions (3, 14)

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