4IED - JenaLib

Asymmetric Unit (Jmol Viewer)

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF FUS-1 (OXA-85), A CLASS D BETA-LACTAMASE FROM FUSOBACTERIUM NUCLEATUM SUBSP. POLYMORPHUM

Authors :   S. Mangani, M. Benvenuti, J. D. Docquier

Date :   13 Dec 12 (Deposition) - 22 Jan 14 (Release) - 22 Jan 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

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 :   Class D Beta-Lactamase, Fus-1, Oxa-85, Antibiotic, Hydrolase, Beta- Lactamase Fold, Beta Lactamase Activity (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Mangani, M. Benvenuti, J. D. Docquier
Crystal Structure Of Fus-1 (Oxa-85), A Class D Beta-Lactamase From Fusobacterium Nucleatum Subsp. Polymorphum
To Be Published
PubMed: search

Molecule 1 - CLASS D BETA-LACTAMASE
	Chains	:	A, B, C, D
	EC Number	:	3.5.2.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Gene	:	FUS1
	Organism Scientific	:	FUSOBACTERIUM NUCLEATUM SUBSP. POLYMORPHUM
	Organism Taxid	:	76857

		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 (5, 21)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	EDO	3	Ligand/Ion	1,2-ETHANEDIOL
3	KCX	4	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
4	MG	12	Ligand/Ion	MAGNESIUM ION
5	NA	1	Ligand/Ion	SODIUM ION

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
3	KCX	1	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
3	KCX	1	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
3	KCX	1	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
3	KCX	1	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (17, 17)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HOH A:565 , HOH A:623 , HOH A:700 , HOH A:782 , HOH A:800 , HOH A:871	BINDING SITE FOR RESIDUE MG A 301
02	AC2	SOFTWARE	HOH A:487 , HOH A:503 , HOH A:578 , HOH A:582 , HOH A:593 , HOH A:613	BINDING SITE FOR RESIDUE MG A 302
03	AC3	SOFTWARE	SER A:92 , HOH A:419 , SER B:92 , HOH B:413	BINDING SITE FOR RESIDUE CL A 303
04	AC4	SOFTWARE	ASP A:91 , HOH A:411 , HOH A:458 , HOH A:477 , HOH A:549 , HOH A:799 , THR B:197 , LEU B:236 , ARG B:239	BINDING SITE FOR RESIDUE EDO A 304
05	AC5	SOFTWARE	MET A:79 , TYR A:82 , ASP A:96 , HOH A:605 , LYS B:187	BINDING SITE FOR RESIDUE EDO A 305
06	AC6	SOFTWARE	ILE B:72 , PHE B:80 , HOH B:477 , HOH D:431	BINDING SITE FOR RESIDUE NA B 301
07	AC7	SOFTWARE	ASN A:134 , GLU A:136 , ASN B:134 , GLU B:136 , HOH B:446	BINDING SITE FOR RESIDUE MG B 302
08	AC8	SOFTWARE	ASP B:35 , ASN B:38 , ASN B:220 , HOH B:522 , HOH B:550 , ASP D:142	BINDING SITE FOR RESIDUE MG B 303
09	AC9	SOFTWARE	GLU B:117 , HOH B:514 , HOH B:527 , HOH B:570 , HOH D:590	BINDING SITE FOR RESIDUE MG B 304
10	BC1	SOFTWARE	ASP B:229 , ILE B:230 , SER B:231 , ASP B:232 , PHE B:235 , HOH B:665 , HOH B:786	BINDING SITE FOR RESIDUE EDO B 305
11	BC2	SOFTWARE	ASN C:134 , GLU C:136 , HOH C:461 , ASN D:134 , GLU D:136	BINDING SITE FOR RESIDUE MG C 301
12	BC3	SOFTWARE	HOH A:627 , HOH A:798 , HOH C:466 , HOH C:766 , HOH C:778 , HOH C:792	BINDING SITE FOR RESIDUE MG C 302
13	BC4	SOFTWARE	SER C:57 , HOH C:465 , HOH C:795	BINDING SITE FOR RESIDUE MG C 303
14	BC5	SOFTWARE	HOH C:493 , HOH C:652 , HOH C:660 , HOH C:662 , HOH C:667 , HOH C:796	BINDING SITE FOR RESIDUE MG C 304
15	BC6	SOFTWARE	ASP B:35 , LYS B:40 , HOH B:452 , HOH D:502	BINDING SITE FOR RESIDUE MG D 301
16	BC7	SOFTWARE	HOH D:431 , HOH D:465 , HOH D:501 , HOH D:516 , HOH D:549 , HOH D:644	BINDING SITE FOR RESIDUE MG D 302
17	BC8	SOFTWARE	GLU D:78 , HOH D:544 , HOH D:565 , HOH D:694 , HOH D:719 , HOH D:804	BINDING SITE FOR RESIDUE MG D 303

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

Asymmetric Unit

No.	Residues
1	Gly A:148	-	Pro A:149
2	Gly B:148	-	Pro B:149
3	Gly C:148	-	Pro C:149
4	Gly D:148	-	Pro D:149

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

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

(no "Exon" information available for 4IED)

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 d4ieda_ A: automated matches                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh..eeeeeee....eeeeehhhhhh....hhhhhhhhhhhhhhhh...................hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhhh.....hhhhhhhhhhhheeee....eeeeeeeee.......eeeeeeeee....eeeeeeeee..hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ied A  13 NENQFMKEIFERKGLNGTFVVYDLKNDKIDYYNLDRANERFYPASSFkIFNTLIGLENGIVKNVDEMFYYYDGSKVFLDSWAKDSNLRYAIKVSQVPAYKKLARELGKERMQEGLNKLNYGNKEIGSEIDKFWLEGPLKISAMEQVKLLNLLSQSKLPFKLENQEQVKDITILEKKDDFILHGKTGWATDNIVVPIGWFVGWIETSDNIYSFAINLDISDSKFLPKREEIVREYFKNINVIK 254
                                    22        32        42        52       |62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252  
                                                                          60-KCX

Chain B from PDB  Type:PROTEIN  Length:245
                                                                                                                                                                                                                                                                                     
               SCOP domains d4iedb_ B: automated matches                                                                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eehhhhhhhhhhhh..eeeeeee....eeeeehhhhhh.ee.hhhhhhhhhhhhhhhh........eee........hhhhh..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....................eehhhhhhhhhhhhh.....hhhhhhhhhhhheeee....eeeeeeeee.......eeeeeeeee....eeeeeeeee..hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ied B  10 SFGNENQFMKEIFERKGLNGTFVVYDLKNDKIDYYNLDRANERFYPASSFkIFNTLIGLENGIVKNVDEMFYYYDGSKVFLDSWAKDSNLRYAIKVSQVPAYKKLARELGKERMQEGLNKLNYGNKEIGSEIDKFWLEGPLKISAMEQVKLLNLLSQSKLPFKLENQEQVKDITILEKKDDFILHGKTGWATDNIVVPIGWFVGWIETSDNIYSFAINLDISDSKFLPKREEIVREYFKNINVIK 254
                                    19        29        39        49        59|       69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249     
                                                                             60-KCX

Chain C from PDB  Type:PROTEIN  Length:247
                                                                                                                                                                                                                                                                                       
               SCOP domains d4iedc_ C: automated matches                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeehhhhhhhhhh....eeeeeee....eeeeehhhhhh.ee.hhhhhhhhhhhhhhhh...................hhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....................eehhhhhhhhhhhhh.....hhhhhhhhhhhheeee....eeeeeeeee.......eeeeeeeee....eeeeeeeee..hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ied C   8 IISFGNENQFMKEIFERKGLNGTFVVYDLKNDKIDYYNLDRANERFYPASSFkIFNTLIGLENGIVKNVDEMFYYYDGSKVFLDSWAKDSNLRYAIKVSQVPAYKKLARELGKERMQEGLNKLNYGNKEIGSEIDKFWLEGPLKISAMEQVKLLNLLSQSKLPFKLENQEQVKDITILEKKDDFILHGKTGWATDNIVVPIGWFVGWIETSDNIYSFAINLDISDSKFLPKREEIVREYFKNINVIK 254
                                    17        27        37        47        57  |     67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       
                                                                               60-KCX

Chain D from PDB  Type:PROTEIN  Length:242
                                                                                                                                                                                                                                                                                  
               SCOP domains d4iedd_ D: automated matches                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh..eeeeeee....eeeeehhhhhh.ee.hhhhhhhhhhhhhhhh........eee........hhhhh..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....................eehhhhhhhhhhhhh.....hhhhhhhhhhhheeee....eeeeeeeee.......eeeeeeeee....eeeeeeeee..hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ied D  13 NENQFMKEIFERKGLNGTFVVYDLKNDKIDYYNLDRANERFYPASSFkIFNTLIGLENGIVKNVDEMFYYYDGSKVFLDSWAKDSNLRYAIKVSQVPAYKKLARELGKERMQEGLNKLNYGNKEIGSEIDKFWLEGPLKISAMEQVKLLNLLSQSKLPFKLENQEQVKDITILEKKDDFILHGKTGWATDNIVVPIGWFVGWIETSDNIYSFAINLDISDSKFLPKREEIVREYFKNINVIK 254
                                    22        32        42        52       |62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252  
                                                                          60-KCX

Legend:		→ Mismatch	(orange background)
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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 '\|'

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)

Fusobacterium nucleatum [TaxId: 76857] (1)

1a	d4ieda_	A:
1b	d4iedb_	B:
1c	d4iedc_	C:
1d	d4iedd_	D:

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

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

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Cis Peptide Bonds
		Gly A:148 - Pro A:149	[ RasMol ]
		Gly B:148 - Pro B:149	[ RasMol ]
		Gly C:148 - Pro C:149	[ RasMol ]
		Gly D:148 - Pro D:149	[ RasMol ]

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Description

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Chains, Units

Ligands, Modified Residues, Ions (5, 21)

Sites (17, 17)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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