8DE1: TEM-1 beta-lactamase A237Y mutant covalently

TEM-1 beta-lactamase A237Y mutant covalently bound to avibactam. Determined by X-ray diffraction at 1.56 Å resolution. Released 7 Sept 2022.

Method: X-ray diffraction
Resolution: 1.56 Å
Organism: Escherichia coli
Chains: 4
Atoms: 9,507
Mol. weight: 117.31 kDa
Ligands: NXL
Released: 7 Sept 2022

Explore 8DE1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8DE1 contains 56 α-helices and 39 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 14 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	27-40	14
β-strand	43-50	8	1
β-strand	56-60	5	1
β-strand	66-67	2	2
α-helix	69-71	3
α-helix	72-85	14
β-strand	94-95	2	3
α-helix	99-101	3
α-helix	109-111	3
β-strand	117-118	2	3
α-helix	119-128	10
α-helix	132-142	11
α-helix	145-154	10
α-helix	168-170	3
β-strand	180-181	2	2
α-helix	183-195	13
α-helix	201-212	12
α-helix	221-224	4
α-helix	225-226	2
β-strand	230-238	9	1
β-strand	242-250	9	1
β-strand	257-264	8	1
α-helix	270-286	17

Chains B, C and D: 14 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	27-40	14
β-strand	43-50	8	4
β-strand	56-60	5	4
β-strand	66-67	2	5
α-helix	69-71	3
α-helix	72-85	14
β-strand	94-95	2	6
α-helix	99-101	3
α-helix	109-111	3
β-strand	117-118	2	6
α-helix	119-128	10
α-helix	132-142	11
α-helix	145-154	10
β-strand	161	1	5
α-helix	168-170	3
β-strand	180-181	2	5
α-helix	183-195	13
α-helix	201-212	12
α-helix	221-224	4
α-helix	225-226	2
β-strand	230-238	9	4
β-strand	242-250	9	4
β-strand	257-264	8	4
α-helix	270-286	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Beta-lactamase TEM	A, B, C, D	protein	264	Escherichia coli	P62593 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>8DE1_1 Beta-lactamase TEM (chains A, B, C, D)
GHPETLVKVKDAEDQLGARVGYIELDLNSGKILESFRPEERFPMMSTFKVLLCGAVLSRV
DAGQEQLGRRIHYSQNDLVEYSPVTEKHLTDGMTVRELCSAAITMSDNTAANLLLTTIGG
PKELTAFLHNMGDHVTRLDRWEPELNEAIPNDERDTTTPAAMATTLRKLLTGELLTLASR
QQLIDWMEADKVAGPLLRSALPAGWFIADKSGYGERGSRGIIAALGPDGKPSRIVVIYTT
GSQATMDERNRQIAEIGASLIKHW

Ligands and cofactors

ID	Name	Formula	Copies
NXL	(2S,5R)-1-formyl-5-[(sulfooxy)amino]piperidine-2-carboxamide	C7 H13 N3 O6 S	4

Primary citation

Protein Electric Fields Enable Faster and Longer-Lasting Covalent Inhibition of beta-Lactamases. Ji, Z., Kozuch, J., Mathews, I.I. et al. J Am Chem Soc (2022) 144:20947-20954. DOI 10.1021/jacs.2c09876 · PubMed

Other PDB entries of the same protein (UniProt P62593 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1M40 0.85 Å, Ultra high resolution crystal structure of tem-1
4ID4 1.05 Å, Crystal structure of chimeric beta-lactamase cTEM-17m
4R4S 1.1 Å, Crystal structure of chimeric beta-lactamase cTEM-19m at 1.1 angstrom resolution
4QY6 1.15 Å, Crystal structures of chimeric beta-lactamase cTEM-19m showing different conformations
1NYM 1.2 Å, Crystal Structure of the complex between M182T mutant of TEM-1 and a boronic acid…
4R4R 1.2 Å, Crystal structure of chimeric beta-lactamase cTEM-19m at 1.2 angstrom resolution
4RX3 1.39 Å, A triple mutant in the omega-loop of TEM-1 beta-lactamase changes the substrate profile…
1YT4 1.4 Å, Crystal structure of TEM-76 beta-lactamase at 1.4 Angstrom resolution
5HW5 1.41 Å, Crystal structure of TEM1 beta-lactamase in the presence of 2.0 MPa xenon
4RVA 1.44 Å, A triple mutant in the omega-loop of TEM-1 beta-lactamase changes the substrate profile…
6AYK 1.44 Å, Crystal structure of TEM1 beta-lactamase mutant I263A in the presence of 1.2 MPa xenon
1PZP 1.45 Å, TEM-1 Beta-Lactamase in Complex with a Novel, Core-Disrupting, Allosteric Inhibitor

Browse structure collections

About this viewer

MolViewer shows 8DE1 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.