2H6A - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE ZINC-BETA-LACTAMASE L1 FROM STENOTROPHOMONAS MALTOPHILIA (MONO ZINC FORM)

Authors :   L. Nauton, G. Garau, R. Kahn, O. Dideberg

Date :   31 May 06 (Deposition) - 17 Apr 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Hydrolase, Metallo, Zn, Lactamase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Nauton, R. Kahn, G. Garau, J. F. Hernandez, O. Dideberg
Structural Insights Into The Design Of Inhibitors For The L1 Metallo-Beta-Lactamase From Stenotrophomonas Maltophilia.
J. Mol. Biol. V. 375 257 2008
PubMed-ID: 17999929 | Reference-DOI: 10.1016/J.JMB.2007.10.036
(for further references see the PDB file header)

Molecule 1 - METALLO-BETA-LACTAMASE L1
	Chains	:	A, B
	EC Number	:	3.5.2.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	STENOTROPHOMONAS MALTOPHILIA
	Organism Taxid	:	40324
	Synonym	:	BETA-LACTAMASE TYPE II, PENICILLINASE

		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, 8)

No.	Name	Count	Type	Full Name
1	SO4	6	Ligand/Ion	SULFATE ION
2	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	SO4	4	Ligand/Ion	SULFATE ION
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:116 , HIS A:118 , HIS A:196 , SO4 A:1106 , HOH A:1308 , HOH A:1311	BINDING SITE FOR RESIDUE ZN A 320
2	AC2	SOFTWARE	HIS B:116 , HIS B:118 , HIS B:196 , SO4 B:1105 , HOH B:1296 , HOH B:1313	BINDING SITE FOR RESIDUE ZN B 321
3	AC3	SOFTWARE	ARG B:172 , VAL B:179 , ILE B:180 , THR B:181 , HOH B:1171 , HOH B:1307 , HOH B:1319	BINDING SITE FOR RESIDUE SO4 B 1101
4	AC4	SOFTWARE	ARG A:172 , VAL A:179 , ILE A:180 , THR A:181 , HOH A:1316	BINDING SITE FOR RESIDUE SO4 A 1102
5	AC5	SOFTWARE	ARG A:102 , HOH A:1158 , HOH A:1212	BINDING SITE FOR RESIDUE SO4 A 1103
6	AC6	SOFTWARE	ARG A:209 , ALA A:275 , ARG A:276 , ALA A:289 , GLY A:290 , ALA A:291 , HOH A:1274 , HOH A:1288 , HOH A:1298 , HOH B:1419	BINDING SITE FOR RESIDUE SO4 A 1104
7	AC7	SOFTWARE	HIS B:196 , SER B:221 , SER B:225 , PRO B:227 , HIS B:263 , ZN B:321 , HOH B:1296 , HOH B:1298 , HOH B:1313 , HOH B:1347 , HOH B:1355	BINDING SITE FOR RESIDUE SO4 B 1105
8	AC8	SOFTWARE	HIS A:196 , SER A:221 , SER A:225 , PRO A:227 , HIS A:263 , ZN A:320 , HOH A:1194 , HOH A:1308 , HOH A:1310 , HOH A:1311 , HOH A:1389 , HOH A:1424	BINDING SITE FOR RESIDUE SO4 A 1106

Asymmetric Unit

No.	Residues
1	A:256	-	A:296
2	B:256	-	B:296

(no "Cis Peptide Bond" information available for 2H6A)

(no "SAP(SNP)/Variant" information available for 2H6A)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BETA_LACTAMASE_B_1	PS00743	Beta-lactamases class B signature 1.	BLA1_STEMA	102-122	2	A:113-133 B:113-133

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BETA_LACTAMASE_B_1	PS00743	Beta-lactamases class B signature 1.	BLA1_STEMA	102-122	1	A:113-133 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BETA_LACTAMASE_B_1	PS00743	Beta-lactamases class B signature 1.	BLA1_STEMA	102-122	1	- B:113-133

(no "Exon" information available for 2H6A)

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:266
 aligned with BLA1_STEMA | P52700 from UniProtKB/Swiss-Prot  Length:290

    Alignment length:266
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282      
           BLA1_STEMA    23 EVPLPQLRAYTVDASWLQPMAPLQIADHTWQIGTEDLTALLVQTPDGAVLLDGGMPQMASHLLDNMKARGVTPRDLRLILLSHAHADHAGPVAELKRRTGAKVAANAESAVLLARGGSDDLHFGDGITYPPANADRIVMDGEVITVGGIVFTAHFMAGHTPGSTAWTWTDTRNGKPVRIAYADSLSAPGYQLQGNPRYPHLIEDYRRSFATVRALPCDVLLTPHPGASNWDYAAGARAGAKALTCKAYADAAEQKFDGQLAKETAG 288
               SCOP domains d2h6aa_ A: automated matches                                                                                                                                                                                                                                               SCOP domains
               CATH domains 2h6aA00 A:24-317 Metallo-beta-lactamase, chain A                                                                                                                                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhh....eeee..eee........eeeee..eeeee...hhhhhhhhhhhhhhh..hhh.eeeee....hhhhhhhhhhhhhhh..eeeehhhhhhhhhh....................ee.....eeee..eeeeeee........eeeeeeeee..eeeeeee..................hhhhhhhhhhhhhhh....eee..hhhhhh....hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------BETA_LACTAMASE_B_1   ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2h6a A  24 EVPLPQLRAYTVDASWLQPMAPLQIADHTWQIGTEDLTALLVQTPDGAVLLDGGMPQMASHLLDNMKARGVTPRDLRLILLSHAHADHAGPVAELKRRTGAKVAANAESAVLLARGGSDDLHFGDGITYPPANADRIVMDGEVITVGGIVFTAHFMAGHTPGSTAWTWTDTRNGKPVRIAYADSLSAPGYQLQGNPRYPHLIEDYRRSFATVRALPCDVLLTPHPGASNWDYAAGARAGAKALTCKAYADAAEQKFDGQLAKETAG 317
                                    33        43        53   ||   72        82    ||  93       103       113       123       133       143       153   ||  165||     176       186    || 197       207       217    || 229       239       249       259       269      |291       301       311      
                                                            57|                  87|                                                                 157|   166|                    191|                          222|                                                276|                            
                                                             67                   89                                                                  160    168                     193                           225                                                 289

Chain B from PDB  Type:PROTEIN  Length:266
 aligned with BLA1_STEMA | P52700 from UniProtKB/Swiss-Prot  Length:290

    Alignment length:266
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282      
           BLA1_STEMA    23 EVPLPQLRAYTVDASWLQPMAPLQIADHTWQIGTEDLTALLVQTPDGAVLLDGGMPQMASHLLDNMKARGVTPRDLRLILLSHAHADHAGPVAELKRRTGAKVAANAESAVLLARGGSDDLHFGDGITYPPANADRIVMDGEVITVGGIVFTAHFMAGHTPGSTAWTWTDTRNGKPVRIAYADSLSAPGYQLQGNPRYPHLIEDYRRSFATVRALPCDVLLTPHPGASNWDYAAGARAGAKALTCKAYADAAEQKFDGQLAKETAG 288
               SCOP domains d2h6ab_ B: automated matches                                                                                                                                                                                                                                               SCOP domains
               CATH domains 2h6aB00 B:24-317 Metallo-beta-lactamase, chain A                                                                                                                                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhh....ee....eee........eeeee..eeeee...hhhhhhhhhhhhhhh..hhh.eeeee....hhhhhhhhhhhhhhh..eeeehhhhhhhhhh....................ee.....eeee..eeeeeee........eeeeeeeee..eeeeeee..................hhhhhhhhhhhhhhh....eee..hhhhhh....hhhhh.....hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------BETA_LACTAMASE_B_1   ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2h6a B  24 EVPLPQLRAYTVDASWLQPMAPLQIADHTWQIGTEDLTALLVQTPDGAVLLDGGMPQMASHLLDNMKARGVTPRDLRLILLSHAHADHAGPVAELKRRTGAKVAANAESAVLLARGGSDDLHFGDGITYPPANADRIVMDGEVITVGGIVFTAHFMAGHTPGSTAWTWTDTRNGKPVRIAYADSLSAPGYQLQGNPRYPHLIEDYRRSFATVRALPCDVLLTPHPGASNWDYAAGARAGAKALTCKAYADAAEQKFDGQLAKETAG 317
                                    33        43        53   ||   72        82    ||  93       103       113       123       133       143       153   ||  165||     176       186    || 197       207       217    || 229       239       249       259       269      |291       301       311      
                                                            57|                  87|                                                                 157|   166|                    191|                          222|                                                276|                            
                                                             67                   89                                                                  160    168                     193                           225                                                 289

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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: Alpha and beta proteins (a+b) (23004)

Fold: Metallo-hydrolase/oxidoreductase (184)

Superfamily: Metallo-hydrolase/oxidoreductase (184)

Family: Zn metallo-beta-lactamase (93)

Protein domain: automated matches (30)

Stenotrophomonas maltophilia [TaxId: 40324] (2)

1a	d2h6aa_	A:
1b	d2h6ab_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 4-Layer Sandwich (459)

Topology: Metallo-beta-lactamase; Chain A (92)

Homologous Superfamily: Metallo-beta-lactamase, chain A (92)

Stenotrophomonas maltophilia. Organism_taxid: 40324. (1)

1a	2h6aA00	A:24-317
1b	2h6aB00	B:24-317

(no "Pfam Domain" information available for 2H6A)

Asymmetric Unit(hide GO term definitions)

Chain A,B (BLA1_STEMA | P52700)

molecular function
	GO:0008800	beta-lactamase activity	Catalysis of the reaction: a beta-lactam + H2O = a substituted beta-amino acid.
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0017001	antibiotic catabolic process	The chemical reactions and pathways resulting in the breakdown of antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.
	GO:0046677	response to antibiotic	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
cellular component
	GO:0042597	periplasmic space	The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Asymmetric Unit
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2fm6	NATIVE FORM
2fu7	CU-SUBSTITUTED FORM
2fu8	D-CAPTOPRIL COMPLEX
2fu9	MP2 INHIBITOR COMPLEX
2gfj	INHIBITOR 1 COMPLEX
2gfk	INHIBITOR 2 COMPLEX

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Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

SS Bonds (2, 2)

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