5HH4 - JenaLib

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Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF METALLO-BETA-LACTAMASE IMP-1 IN COMPLEX WITH A PHOSPHONATE-BASED INHIBITOR

Authors :   P. Hinchliffe, J. Spencer

Date :   09 Jan 16 (Deposition) - 18 Jan 17 (Release) - 18 Jan 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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 :   Inhibitor, Carbapenamase, Pyridine, Phosphonate, Antibiotic Resistance, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Hinchliffe, C. A. Tanner, G. Labbe, V. J. Goodfellow, A. P. Krismanich, E. E. Whittle, J. Spencer, G. I. Dmitrienko
Structural Basis Of Metallo-Beta-Lactamase Inhibition By Phosphonates
To Be Published
PubMed: search

Molecule 1 - BETA-LACTAMASE IMP-1
	Chains	:	A, B, C, D
	EC Number	:	3.5.2.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	SOLUBL21
	Organism Scientific	:	SERRATIA MARCESCENS
	Organism Taxid	:	615
	Synonym	:	BLAIMP,BETA-LACTAMASE TYPE II,PENICILLINASE, CLASS B1 METALLO-BETA-LACTAMASE IMP-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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 14)

No.	Name	Count	Type	Full Name
1	60M	2	Ligand/Ion	6-(PHOSPHONOMETHYL)PYRIDINE-2-CARBOXYLIC ACID
2	CL	1	Ligand/Ion	CHLORIDE ION
3	EDO	3	Ligand/Ion	1,2-ETHANEDIOL
4	ZN	8	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	60M	1	Ligand/Ion	6-(PHOSPHONOMETHYL)PYRIDINE-2-CARBOXYLIC ACID
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
4	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	60M	1	Ligand/Ion	6-(PHOSPHONOMETHYL)PYRIDINE-2-CARBOXYLIC ACID
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
4	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	60M	-1	Ligand/Ion	6-(PHOSPHONOMETHYL)PYRIDINE-2-CARBOXYLIC ACID
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
4	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	60M	-1	Ligand/Ion	6-(PHOSPHONOMETHYL)PYRIDINE-2-CARBOXYLIC ACID
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
4	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:77 , HIS A:79 , HIS A:139 , ZN A:302 , HOH A:422	binding site for residue ZN A 301
02	AC2	SOFTWARE	ASP A:81 , CYS A:158 , HIS A:197 , ZN A:301 , 60M A:303 , HOH A:422	binding site for residue ZN A 302
03	AC3	SOFTWARE	VAL A:25 , HIS A:79 , SER A:80 , ASP A:81 , HIS A:139 , CYS A:158 , LYS A:161 , GLY A:166 , ASN A:167 , HIS A:197 , ZN A:302 , HOH A:422 , HOH A:433 , HOH A:435 , EDO D:303	binding site for residue 60M A 303
04	AC4	SOFTWARE	ASP B:81 , CYS B:158 , HIS B:197 , ZN B:302 , 60M B:303 , HOH B:479	binding site for residue ZN B 301
05	AC5	SOFTWARE	HIS B:77 , HIS B:79 , HIS B:139 , ZN B:301 , HOH B:479	binding site for residue ZN B 302
06	AC6	SOFTWARE	VAL B:25 , HIS B:79 , SER B:80 , ASP B:81 , HIS B:139 , CYS B:158 , LYS B:161 , GLY B:166 , ASN B:167 , HIS B:197 , ZN B:301 , HOH B:479 , HOH B:494 , HOH B:499	binding site for residue 60M B 303
07	AC7	SOFTWARE	GLU B:43 , THR B:52 , LYS B:54 , LYS B:69 , HOH B:430 , HOH B:545	binding site for residue CL B 304
08	AC8	SOFTWARE	SER B:198 , GLU B:199 , HOH B:418 , VAL C:200 , GLY C:201 , ASP C:202 , SER C:204 , LEU C:205 , HOH C:414	binding site for residue EDO B 305
09	AC9	SOFTWARE	HIS C:77 , HIS C:79 , HIS C:139 , ZN C:302 , HOH C:524	binding site for residue ZN C 301
10	AD1	SOFTWARE	ASP C:81 , CYS C:158 , HIS C:197 , ZN C:301 , HOH C:465 , HOH C:524	binding site for residue ZN C 302
11	AD2	SOFTWARE	GLU C:14 , GLY C:15 , VAL C:38 , LEU C:39 , GLU C:150 , HOH C:416	binding site for residue EDO C 303
12	AD3	SOFTWARE	HIS D:77 , HIS D:79 , HIS D:139 , ZN D:302 , HOH D:456	binding site for residue ZN D 301
13	AD4	SOFTWARE	ASP D:81 , CYS D:158 , HIS D:197 , ZN D:301 , HOH D:456 , HOH D:458	binding site for residue ZN D 302
14	AD5	SOFTWARE	HIS A:197 , 60M A:303 , GLU D:199 , HOH D:422	binding site for residue EDO D 303

(no "SS Bond" information available for 5HH4)

Asymmetric Unit

No.	Residues
1	Gly D:84	-	Gly D:85

(no "SAP(SNP)/Variant" information available for 5HH4)

(no "PROSITE Motif" information available for 5HH4)

(no "Exon" information available for 5HH4)

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:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee..eeeeeeeeee...eeeeeeeeeeee..eeeee....hhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhh...eeeehhhhhhhhhh......eeee..eeeee...eeee...........eeee....eeeeehhh..............hhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hh4 A   3 SLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNES 220
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212

Chain B from PDB  Type:PROTEIN  Length:222
                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeeeee..eeeeeeeeee...eeeeeeeeeee...eeeee....hhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhh...eeeehhhhhhhhhh......eee...eeeee...eeee...........eeee....eeeeehhh..............hhhhhhhhhhhhh....eeee.......hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5hh4 B  -1 GPAESLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNES 220
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218

Chain C from PDB  Type:PROTEIN  Length:222
                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee..eeeeeeeeee...eeeeeeeeeeee..eeeee....hhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhh...eeeehhhhhhhhhh......eee...eeeee...eeee...........eee.....eeeeehhh..............hhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5hh4 C   4 LPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNESKKPSN 225
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223

Chain D from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee..eeeeeeeeee...eeeeeeeeeee...eeeee....hhhhhhhhhhhhhh...eeeeee..........hhhhhhhh...eeeehhhhhhhhhh......eee...eeeee...eeee...........eeee....eeeeehhh..............hhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hh4 D   3 SLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNE 219
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212

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 '\|'

(no "SCOP Domain" information available for 5HH4)

(no "CATH Domain" information available for 5HH4)

(no "Pfam Domain" information available for 5HH4)

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	Cis Peptide Bonds
		Gly D:84 - Gly D:85	[ RasMol ]

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(no "Related Entries Specified in the PDB File" available for 5HH4)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 14)

Sites (14, 14)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (7, 7)

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