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Title :   CRYSTAL STRUCTURE OF THE GES-1 IMIPENEM ACYL-ENZYME COMPLEX

Authors :   C. A. Smith, S. B. Vakulenko, J. Munoz

Date :   20 Aug 12 (Deposition) - 24 Jul 13 (Release) - 24 Jul 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.10

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

Keywords :   Beta-Lactamase, Carbapenemase, Imipenem, Hydrolase-Antibiotic Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. A. Smith, H. Frase, M. Toth, M. Kumarasiri, K. Wiafe, J. Munoz, S. Mobashery, S. B. Vakulenko
Structural Basis For Progression Toward The Carbapenemase Activity In The Ges Family Of Beta-Lactamases.
J. Am. Chem. Soc. V. 134 19512 2012
PubMed-ID: 23148776 | Reference-DOI: 10.1021/JA308197J

Molecule 1 - BETA-LACTAMASE GES-1
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	GES-1, BLAGES-1
	Organism Scientific	:	KLEBSIELLA PNEUMONIAE
	Organism Taxid	:	573
	Synonym	:	GES-1 EXTENDED-SPECTRUM BETA-LACTAMASE

		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, 23)

No.	Name	Count	Type	Full Name
1	IM2	2	Ligand/Ion	(5R)-5-[(1S,2R)-1-FORMYL-2-HYDROXYPROPYL]-3-[(2-{[(E)-IMINOMETHYL]AMINO}ETHYL)SULFANYL]-4,5-DIHYDRO-1H-PYRROLE-2-CARBOXYLIC ACID
2	IOD	19	Ligand/Ion	IODIDE ION
3	NA	2	Ligand/Ion	SODIUM ION

Biological Unit 1 (2, 9)

No.	Name	Count	Type	Full Name
1	IM2	1	Ligand/Ion	(5R)-5-[(1S,2R)-1-FORMYL-2-HYDROXYPROPYL]-3-[(2-{[(E)-IMINOMETHYL]AMINO}ETHYL)SULFANYL]-4,5-DIHYDRO-1H-PYRROLE-2-CARBOXYLIC ACID
2	IOD	8	Ligand/Ion	IODIDE ION
3	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (2, 12)

No.	Name	Count	Type	Full Name
1	IM2	1	Ligand/Ion	(5R)-5-[(1S,2R)-1-FORMYL-2-HYDROXYPROPYL]-3-[(2-{[(E)-IMINOMETHYL]AMINO}ETHYL)SULFANYL]-4,5-DIHYDRO-1H-PYRROLE-2-CARBOXYLIC ACID
2	IOD	11	Ligand/Ion	IODIDE ION
3	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (18, 18)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	CYS A:63 , SER A:64 , SER A:125 , ASN A:127 , GLU A:161 , LYS A:229 , THR A:230 , GLY A:231 , THR A:232 , ARG A:238 , HOH A:646 , HOH A:764	BINDING SITE FOR RESIDUE IM2 A 501
02	AC2	SOFTWARE	MET A:56	BINDING SITE FOR RESIDUE IOD A 503
03	AC3	SOFTWARE	ARG A:204	BINDING SITE FOR RESIDUE IOD A 504
04	AC4	SOFTWARE	LYS A:222 , IOD B:511	BINDING SITE FOR RESIDUE IOD A 506
05	AC5	SOFTWARE	ARG A:105 , GLN B:210	BINDING SITE FOR RESIDUE IOD A 507
06	AC6	SOFTWARE	NA A:510	BINDING SITE FOR RESIDUE IOD A 508
07	AC7	SOFTWARE	PRO A:93 , ASP A:94 , IOD A:508	BINDING SITE FOR RESIDUE NA A 510
08	AC8	SOFTWARE	CYS B:63 , SER B:64 , SER B:125 , ASN B:127 , GLU B:161 , LYS B:229 , THR B:230 , GLY B:231 , THR B:232 , ARG B:238 , HOH B:668 , HOH B:778	BINDING SITE FOR RESIDUE IM2 B 501
09	AC9	SOFTWARE	ARG B:204	BINDING SITE FOR RESIDUE IOD B 502
10	BC1	SOFTWARE	HOH B:671	BINDING SITE FOR RESIDUE IOD B 503
11	BC2	SOFTWARE	CYS B:233 , GLY B:236 , GLY B:237 , ARG B:267 , HOH B:618	BINDING SITE FOR RESIDUE IOD B 505
12	BC3	SOFTWARE	THR B:177 , ILE B:179	BINDING SITE FOR RESIDUE IOD B 506
13	BC4	SOFTWARE	GLN B:145 , LYS B:149 , GLN B:280	BINDING SITE FOR RESIDUE IOD B 507
14	BC5	SOFTWARE	GLN A:210 , ARG B:105	BINDING SITE FOR RESIDUE IOD B 508
15	BC6	SOFTWARE	ILE B:150 , LYS B:187	BINDING SITE FOR RESIDUE IOD B 509
16	BC7	SOFTWARE	THR B:113 , HOH B:666	BINDING SITE FOR RESIDUE IOD B 510
17	BC8	SOFTWARE	IOD A:506 , PRO B:93	BINDING SITE FOR RESIDUE IOD B 511
18	BC9	SOFTWARE	GLY B:92 , ASP B:94 , ARG B:135	BINDING SITE FOR RESIDUE NA B 513

Asymmetric Unit

No.	Residues
1	A:63	-	A:233
2	B:63	-	B:233

Asymmetric Unit

No.	Residues
1	Glu A:161	-	Pro A:162
2	Glu B:161	-	Pro B:162

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

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

(no "Exon" information available for 4GOG)

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
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Chain A from PDB  Type:PROTEIN  Length:268
                                                                                                                                                                                                                                                                                                            
               SCOP domains d4goga_ A: automated matches                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh.eeeeeee.....eeeee.....ee.hhhhhhhhhhhhhhhhhhh......eee.hhhhh...hhhhhhhh...eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhhh...hhhhhhhhhhhhhh......hhhhhh....eeeeeeeee...eeeeeeeeee..eeeeeeeeee....hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gog A  19 SEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMGDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILSTD 286
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278

Chain B from PDB  Type:PROTEIN  Length:266
                                                                                                                                                                                                                                                                                                          
               SCOP domains d4gogb_ B: automated matches                                                                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh.eeeeeee.....eeeee.....ee.hhhhhhhhhhhhhhhhhh.......eee.hhhhh...hhhhhhhh...eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhh........eehhhhhhhhhhhhhhh...hhhhhhhhhhhhhh......hhhhhh....eeeeeeeee...eeeeeeeeee..eeeeeeeeee....hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gog B  19 SEKLTFKTDLEKLEREKAAQIGVAIVDPQGEIVAGHRMAQRFAMCSTFKFPLAALVFERIDSGTERGDRKLSYGPDMIVEWSPATERFLASGHMTVLEAAQAAVQLSDNGATNLLLREIGGPAAMTQYFRKIGDSVSRLDRKEPEMGDNTPGDLRDTTTPIAMARTVAKVLYGGALTSTSTHTIERWLIGNQTGDATLRAGFPKDWVVGEKTGTCANGGRNDIGFFKAQERDYAVAVYTTAPKLSAVERDELVASVGQVITQLILS 284
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278

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)

Klebsiella pneumoniae (2)

1a	d4goga_	A:
1b	d4gogb_	B:

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

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

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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		Glu A:161 - Pro A:162	[ RasMol ]
		Glu B:161 - Pro B:162	[ RasMol ]

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4gnu	GES-5 APO FORM
4h8r

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 23)

Sites (18, 18)

SS Bonds (2, 2)

Cis Peptide Bonds (2, 2)

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