3RKK - JenaLib

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Title :   CRYSTAL STRUCTURE OF NEW DELHI METALLO-BETA-LACTAMASE-1 FROM KLEBSIELLA PNEUMONIAE

Authors :   Y. Kim, C. Tesar, R. Jedrzejczak, T. A. Binkowski, G. Babnigg, J. Sacche A. Joachimiak, Midwest Center For Structural Genomics (Mcsg), Structures Of Mtb Proteins Conferring Susceptibility To Kno Inhibitors (Mtbi)

Date :   18 Apr 11 (Deposition) - 18 May 11 (Release) - 28 Mar 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.35

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

Keywords :   Structural Genomics, Psi-Biology, Midwest Center For Structural Genomics, Mcsg, Alpha-Beta Structure, Hydrolase, Structures Of Mtb Proteins Conferring Susceptibility To Known Mtb Inhibitors, Mtbi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Kim, C. Tesar, J. Mire, R. Jedrzejczak, A. Binkowski, G. Babnigg, J. Sacchettini, A. Joachimiak
Structure Of Apo- And Monometalated Forms Of Ndm-1 A Highly Potent Carbapenem-Hydrolyzing Metallo-Beta-Lactamase
Plos One V. 6 24621 2011
PubMed-ID: 21931780 | Reference-DOI: 10.1371/JOURNAL.PONE.0024621

Molecule 1 - BETA-LACTAMASE NDM-1
	Chains	:	A, B
	EC Number	:	3.5.2.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMCSG7
	Expression System Strain	:	BL21 MAGIC
	Expression System Taxid	:	51163
	Expression System Vector Type	:	PLASMID
	Fragment	:	SEQUENCE DATABASE RESIDUES 39-270
	Gene	:	BLANDM-1
	Mutation	:	YES
	Organism Scientific	:	KLEBSIELLA PNEUMONIAE
	Organism Taxid	:	573
	Synonym	:	NDM-1, METALLO-BETA-LACTAMASE NDM-1

		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 (3, 13)

No.	Name	Count	Type	Full Name
1	ACY	1	Ligand/Ion	ACETIC ACID
2	GOL	6	Ligand/Ion	GLYCEROL
3	SO4	6	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 7)

No.	Name	Count	Type	Full Name
1	ACY	-1	Ligand/Ion	ACETIC ACID
2	GOL	4	Ligand/Ion	GLYCEROL
3	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 6)

No.	Name	Count	Type	Full Name
1	ACY	1	Ligand/Ion	ACETIC ACID
2	GOL	2	Ligand/Ion	GLYCEROL
3	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:189 , LYS A:211 , LEU A:218 , GLY A:219 , ASN A:220 , HIS A:250 , HOH A:329	BINDING SITE FOR RESIDUE SO4 A 281
02	AC2	SOFTWARE	LYS A:211 , ASP A:212 , MET A:248 , HIS A:250 , SER A:251 , HOH A:272	BINDING SITE FOR RESIDUE SO4 A 282
03	AC3	SOFTWARE	ARG A:234 , ARG A:264 , HOH A:326	BINDING SITE FOR RESIDUE SO4 A 283
04	AC4	SOFTWARE	HOH A:1 , GLN A:44 , GOL A:285	BINDING SITE FOR RESIDUE GOL A 284
05	AC5	SOFTWARE	HOH A:1 , GOL A:284	BINDING SITE FOR RESIDUE GOL A 285
06	AC6	SOFTWARE	GLN A:53 , ALA A:55 , PRO A:56	BINDING SITE FOR RESIDUE GOL A 286
07	AC7	SOFTWARE	ALA A:55 , PRO A:56 , ASN A:57 , GLY A:200 , THR A:201 , HOH A:300	BINDING SITE FOR RESIDUE GOL A 271
08	AC8	SOFTWARE	THR A:94 , GLY A:127 , ASP B:95 , GLY B:127 , HOH B:346	BINDING SITE FOR RESIDUE SO4 B 281
09	AC9	SOFTWARE	ASP B:212 , MET B:248 , HIS B:250 , SER B:251	BINDING SITE FOR RESIDUE SO4 B 282
10	BC1	SOFTWARE	ARG B:234 , ARG B:264 , HOH B:295	BINDING SITE FOR RESIDUE SO4 B 283
11	BC2	SOFTWARE	GLN B:53 , ALA B:55 , PRO B:56	BINDING SITE FOR RESIDUE GOL B 285
12	BC3	SOFTWARE	HOH B:303 , HOH B:304	BINDING SITE FOR RESIDUE GOL B 286
13	BC4	SOFTWARE	HIS B:120 , ASP B:124 , CYS B:208 , SER B:249 , HIS B:250	BINDING SITE FOR RESIDUE ACY B 287

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

(no "Cis Peptide Bond" information available for 3RKK)

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

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

(no "Exon" information available for 3RKK)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	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:227
 aligned with BLAN1_KLEPN | C7C422 from UniProtKB/Swiss-Prot  Length:270

    Alignment length:227
                                    53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       
          BLAN1_KLEPN    44 QRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR 270
               SCOP domains d3rkka_ A: automated matches                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee..eeeeeee.........eeeeeeee....eeee....hhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhh.eeeeehhhhhhhhhhh.....eee..................eeee...........eeee....eee..............hhhhh...hhhhhhhhhhhhh....eee........hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rkk A  44 QRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR 270
                                    53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263

Chain B from PDB  Type:PROTEIN  Length:226
 aligned with BLAN1_KLEPN | C7C422 from UniProtKB/Swiss-Prot  Length:270

    Alignment length:226
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264      
          BLAN1_KLEPN    45 RFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR 270
               SCOP domains d3rkkb_ B: automated matches                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------Lactamase_B-3rkkB01 B:70-250                                                                                                                                                         -------------------- Pfam domains (1)
           Pfam domains (2) -------------------------Lactamase_B-3rkkB02 B:70-250                                                                                                                                                         -------------------- Pfam domains (2)
         Sec.struct. author .....eeeeee..eeeeeeeeee...eeeeeeeeeeee..eeeee....hhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhh..eeeeehhhhhhhhhh......eee..................eeee...........eeee....eeeee....................hhhhhhhhhhhhh....eeee.......hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rkk B  45 RFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR 270
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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: Alpha and beta proteins (a+b) (23004)

Fold: Metallo-hydrolase/oxidoreductase (184)

Superfamily: Metallo-hydrolase/oxidoreductase (184)

Family: automated matches (42)

Protein domain: automated matches (42)

Klebsiella pneumoniae [TaxId: 573] (21)

1a	d3rkka_	A:
1b	d3rkkb_	B:

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Metallo-HOrase (67)

Family: Lactamase_B (53)

Klebsiella pneumoniae (6)

1a	Lactamase_B-3rkkB01	B:70-250
1b	Lactamase_B-3rkkB02	B:70-250

Asymmetric Unit(hide GO term definitions)

Chain A,B (BLAN1_KLEPN | C7C422)

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).

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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3rkk)

Biological Units
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	3rkk
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3rkj	THE SAME PROTEIN AND THE CRYSTAL FROM DIFFERENT CONDITION. RELATED ID: APC105101 RELATED DB: TARGETDB

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 13)

Sites (13, 13)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (7, 7)

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