4GYQ - JenaLib

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Biological Unit 6 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF NEW DELHI METALLO-BETA-LACTAMASE-1 D223A MUTANT FROM KLEBSIELLA PNEUMONIAE

Authors :   Y. Kim, C. Tesar, R. Jedrzejczak, J. Babnigg, T. A. Binkowski, J. Mire, J. Sacchettini, A. Joachimiak, Mcsg, Midwest Center For Structur Genomics (Mcsg), Structures Of Mtb Proteins Conferring Susce To Known Mtb Inhibitors (Mtbi)

Date :   05 Sep 12 (Deposition) - 26 Sep 12 (Release) - 26 Sep 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.35

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)
Biol. Unit 5: A,B  (1x)
Biol. Unit 6: C,D  (1x)

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

Reference :   Y. Kim, C. Tesar, R. Jedrzejczak, J. Babnigg, T. A. Binkowski, J. Mire, J. Sacchettini, A. Joachimiak
Crystal Structure Of New Delhi Metallo-Beta-Lactamase-1 D223A Mutant From Klebsiella Pneumoniae
To Be Published 2012
PubMed: search

Molecule 1 - BETA-LACTAMASE NDM-1
	Chains	:	A, B, C, D
	EC Number	:	3.5.2.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMCSG7
	Expression System Strain	:	BL21 MAGIC
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	BLANDM-1
	Mutation	:	YES
	Organism Scientific	:	KLEBSIELLA PNEUMONIAE
	Organism Taxid	:	573
	Synonym	:	NDM-1, METALLO-BETA-LACTAMASE NDM-1

		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
Biological Unit 5 (1x)	:	A	B
Biological Unit 6 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	EDO	3	Ligand/Ion	1,2-ETHANEDIOL
2	MG	1	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 5 (1, 3)

No.	Name	Count	Type	Full Name
1	EDO	3	Ligand/Ion	1,2-ETHANEDIOL
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 6 (0, 0)

No.	Name	Count	Type	Full Name
1	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:47 , ASP A:48 , LEU A:49 , ASP A:96 , GLN A:97 , GLN A:100 , ARG B:45	BINDING SITE FOR RESIDUE EDO A 301
2	AC2	SOFTWARE	ILE A:198 , THR A:201 , ASP A:202 , ILE A:203 , ALA A:243	BINDING SITE FOR RESIDUE EDO A 302
3	AC3	SOFTWARE	ASP B:66 , MET B:126 , HOH B:614	BINDING SITE FOR RESIDUE EDO B 301
4	AC4	SOFTWARE	GLY C:178 , HOH C:481 , HOH C:501 , HOH C:584 , HOH C:591	BINDING SITE FOR RESIDUE MG C 301

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

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

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

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

(no "Exon" information available for 4GYQ)

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:236
                                                                                                                                                                                                                                                                            
               SCOP domains d4gyqa_ A: automated matches                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh....eee..eeeeeee..eeeeeeeeee...eeeeeeeeeeee..eeeee....hhhhhhhhhhhhhhhh...eeeeee......hhhhhhhh..eeeeehhhhhhhhhhh.....eee........hhhhh.....eeee...........eeee....eee......................hhhhhhhhhhhhh....eee........hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gyq A  32 RPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGAADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR 270
                                    41        51        61        71        81        91       101       111       121||     134       144       154       164       174       184       194       204       214       224       234       244       254       264      
                                                                                                                    122|                                                                                                                                                
                                                                                                                     126

Chain B from PDB  Type:PROTEIN  Length:232
                                                                                                                                                                                                                                                                        
               SCOP domains d4gyqb_ B: automated matches                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee..eeeeeee..eeeeeeeeee...eeeeeeeeeeee..eeeee....hhhhhhhhhhhhhhhh...eeeeee.........hhhhhhhh..eeeeehhhhhhhhhhh.....eee........hhhhh.....eeee...........eeee....eee......................hhhhhhhhhhhhh....eee........hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gyq B  39 METGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGAADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR 270
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268

Chain C from PDB  Type:PROTEIN  Length:237
                                                                                                                                                                                                                                                                             
               SCOP domains d4gyqc_ C: automated matches                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh....eee..eeeeeee..eeeeeeeeee...eeeeeeeeeeee..eeeee....hhhhhhhhhhhhhhhh...eeeeee.........hhhhhhhh..eeeeehhhhhhhhhhh.....eee........hhhhh.....eeee...........eeee....eee......................hhhhhhhhhhhhh....eee........hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gyq C  34 TIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGAADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR 270
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263

Chain D from PDB  Type:PROTEIN  Length:230
                                                                                                                                                                                                                                                                      
               SCOP domains d4gyqd_ D: automated matches                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee..eeeeeee..eeeeeeeeee...eeeeeeeeeeee..eeeee....hhhhhhhhhhhhhhhh...eeeeee........hhhhhhhhh..eeeeehhhhhhhhhhh.....eee........hhhhh.....eeee...........eeee....eee......................hhhhhhhhhhhhh....eee........hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gyq D  41 TGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGAADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR 270
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270

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(

)

Folds(

)

Superfamilies( (-)

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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	d4gyqa_	A:
1b	d4gyqb_	B:
1c	d4gyqc_	C:
1d	d4gyqd_	D:

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

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

Asymmetric Unit(hide GO term definitions)

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3rkj	NDM1, DELTA-38 CONSTRUCT
3rkk	NDM1, DELTA-36NY CONSTRUCT
3sbl	NDM1, DELTA-36NY CONSTRUCT, DIFFERENT CRYSTALS FORM
3sfp	NDM1, DELTA-36NY CONSTRUCT, ONE-ZN-BOUND
3srx	NDM1, DELTA-36NY CONSTRUCT, TWO CD-BOUND RELATED ID: MCSG-APC105101 RELATED DB: TARGETTRACK

Description

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Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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SCOP Domains (1, 4)

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Gene Ontology (7, 7)

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