5DVA - JenaLib

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Title :   FRAGMENTS BOUND TO THE OXA-48 BETA-LACTAMASE: COMPOUND 1

Authors :   B. A. Lund, T. Christopeit, H. -K. S. Leiros

Date :   21 Sep 15 (Deposition) - 01 Jun 16 (Release) - 22 Jun 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Hydrolase, Inhibitor, Complex, Fragment, Lactamase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. A. Lund, T. Christopeit, Y. Guttormsen, A. Bayer, H. K. Leiros
Screening And Design Of Inhibitor Scaffolds For The Antibiotic Resistance Oxacillinase-48 (Oxa-48) Through Surface Plasmon Resonance Screening.
J. Med. Chem. V. 59 5542 2016
PubMed-ID: 27165692 | Reference-DOI: 10.1021/ACS.JMEDCHEM.6B00660

Molecule 1 - BETA-LACTAMASE
	Chains	:	A, B, C, D
	EC Number	:	3.5.2.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector	:	PDEST17
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 22-265
	Gene	:	BLA OXA-48, BLAOXA-48, KPE71T_00045
	Organism Scientific	:	KLEBSIELLA PNEUMONIAE
	Organism Taxid	:	573

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 10)

No.	Name	Count	Type	Full Name
1	5FL	4	Ligand/Ion	3-(PYRIDIN-4-YL)BENZOIC ACID
2	CL	2	Ligand/Ion	CHLORIDE ION
3	KCX	4	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	5FL	1	Ligand/Ion	3-(PYRIDIN-4-YL)BENZOIC ACID
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	KCX	1	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	5FL	1	Ligand/Ion	3-(PYRIDIN-4-YL)BENZOIC ACID
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	KCX	1	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID

Biological Unit 3 (2, 2)

No.	Name	Count	Type	Full Name
1	5FL	1	Ligand/Ion	3-(PYRIDIN-4-YL)BENZOIC ACID
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	KCX	1	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID

Biological Unit 4 (2, 2)

No.	Name	Count	Type	Full Name
1	5FL	1	Ligand/Ion	3-(PYRIDIN-4-YL)BENZOIC ACID
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	KCX	1	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:70 , SER A:118 , THR A:209 , GLY A:210 , TYR A:211 , ARG A:250 , HOH A:562	binding site for residue 5FL A 301
2	AC2	SOFTWARE	SER B:70 , SER B:118 , THR B:209 , GLY B:210 , TYR B:211 , ARG B:250	binding site for residue 5FL B 301
3	AC3	SOFTWARE	ARG B:206 , HOH B:515 , HOH B:516	binding site for residue CL B 302
4	AC4	SOFTWARE	SER C:70 , SER C:118 , VAL C:120 , THR C:209 , GLY C:210 , TYR C:211 , LEU C:247 , ARG C:250 , HOH C:407 , HOH C:415 , HOH C:418	binding site for residue 5FL C 301
5	AC5	SOFTWARE	ARG A:206 , ARG C:206	binding site for residue CL C 302
6	AC6	SOFTWARE	SER D:70 , ILE D:102 , TRP D:105 , SER D:118 , THR D:209 , TYR D:211 , THR D:213 , SER D:244 , ARG D:250 , HOH D:406 , HOH D:535	binding site for residue 5FL D 301

(no "SS Bond" information available for 5DVA)

Asymmetric Unit

No.	Residues
1	Glu A:216	-	Pro A:217
2	Glu B:216	-	Pro B:217
3	Glu C:216	-	Pro C:217
4	Glu D:216	-	Pro D:217

(no "SAP(SNP)/Variant" information available for 5DVA)

(no "PROSITE Motif" information available for 5DVA)

(no "Exon" information available for 5DVA)

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:242
                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...hhhhhhh....eeeeeee....eeee.hhhhhh....hhhhhhhhhhhhhhhh..................hhhhh...hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhh....hhhhhhhhhhhhhh.....hhhhhhhhhhhheeee....eeeeeeeee......eeeeeeeee....eeeeeeeee..hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dva A  24 EWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFkIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP 265
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263  
                                                                            73-KCX

Chain B from PDB  Type:PROTEIN  Length:242
                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhh.....eeeeeee....eeee...hhhh.ee.hhhhhhhhhhhhhhhh..................hhhhh...hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhh...eehhhhhhhhhhhhh.....hhhhhhhhhhhheeee....eeeeeeeee......eeeeeeeee....eeeeeeeee..hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dva B  24 EWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFkIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP 265
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263  
                                                                            73-KCX

Chain C from PDB  Type:PROTEIN  Length:242
                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhh...eeeeeee....eeee.hhhhhh....hhhhhhhhhhhhhhhh..................hhhhh...hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhh....hhhhhhhhhhhhhh.....hhhhhhhhhhhheeee....eeeeeeeee......eeeeeeeee....eeeeeeeee..hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dva C  24 EWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFkIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP 265
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263  
                                                                            73-KCX

Chain D from PDB  Type:PROTEIN  Length:242
                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...hhhhhhh....eeeeeee....eeee.hhhhhh....hhhhhhhhhhhhhhhh..................hhhhh...hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhh....hhhhhhhhhhhhhh.....hhhhhhhhhhhheeee....eeeeeeeee......eeeeeeeee....eeeeeeeee..hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dva D  24 EWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPASTFkIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP 265
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263  
                                                                            73-KCX

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 '\|'

(no "SCOP Domain" information available for 5DVA)

(no "CATH Domain" information available for 5DVA)

(no "Pfam Domain" information available for 5DVA)

Asymmetric Unit(hide GO term definitions)

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	Ligands, Modified Residues, Ions
		5FL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		KCX	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
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		AC2	[ RasMol ]	+environment [ RasMol ]
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		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Glu A:216 - Pro A:217	[ RasMol ]
		Glu B:216 - Pro B:217	[ RasMol ]
		Glu C:216 - Pro C:217	[ RasMol ]
		Glu D:216 - Pro D:217	[ RasMol ]

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4s2p	4S2P CONTAINS THE APO-FORM OF THE SAME PROTEIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 10)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (5, 5)

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