7AZE: Beta sliding clamp

DNA polymerase sliding clamp from Escherichia coli with peptide 18 bound. Determined by X-ray diffraction at 1.82 Å resolution. Released 1 Dec 2021.

Method: X-ray diffraction
Resolution: 1.82 Å
Organisms: Escherichia coli 2-427-07_S4_C3, synthetic construct
Chains: 4
Atoms: 6,697
Mol. weight: 88.25 kDa
Ligands: MLI
Released: 1 Dec 2021

Explore 7AZE in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7AZE contains 31 α-helices and 54 β-strands across 2 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: 15 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	1
α-helix	7-17	11
α-helix	28-31	4
β-strand	32-38	7	2
β-strand	41-47	7	2
β-strand	51-58	8	2
β-strand	64	1	1
β-strand	66-71	6	2
α-helix	72-81	10
α-helix	83	1
β-strand	87-93	7	1
β-strand	96-101	6	1
β-strand	104-109	6	1
β-strand	111	1	2
α-helix	113-115	3
α-helix	119-121	3
β-strand	126-130	5	2
α-helix	132-140	9
α-helix	143-145	3
α-helix	153-155	3
β-strand	157-172	16	3
β-strand	176-196	21	3
α-helix	197-205	9
α-helix	213	1
β-strand	214-218	5	2
β-strand	222-227	6	2
β-strand	230-235	6	2
α-helix	236	1
β-strand	237	1	3
α-helix	244-247	4
β-strand	254-259	6	3
α-helix	260-271	12
β-strand	280-286	7	4
β-strand	289-295	7	4
β-strand	301-307	7	4
β-strand	309	1	3
β-strand	315-320	6	4
α-helix	321-330	10
β-strand	335-340	6	3
β-strand	347-351	5	3
β-strand	354-361	8	3
β-strand	364	1	4

Chain B: 16 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	4
α-helix	7-17	11
α-helix	29-31	3
β-strand	32-38	7	5
β-strand	41-47	7	5
β-strand	51-58	8	5
β-strand	64	1	4
β-strand	66-71	6	5
α-helix	72-81	10
α-helix	83	1
β-strand	87-93	7	4
β-strand	96-101	6	4
β-strand	104-109	6	4
β-strand	111	1	5
α-helix	113-115	3
α-helix	119-121	3
β-strand	126-130	5	5
α-helix	132-140	9
α-helix	143-145	3
α-helix	153-155	3
β-strand	157-172	16	6
β-strand	176-196	21	6
α-helix	197-206	10
α-helix	213	1
β-strand	214-218	5	5
β-strand	222-227	6	5
β-strand	230-235	6	5
α-helix	236	1
β-strand	237	1	6
α-helix	238	1
α-helix	244-247	4
β-strand	254-259	6	6
α-helix	260-271	12
β-strand	280-286	7	1
β-strand	289-295	7	1
β-strand	301-307	7	1
β-strand	309	1	6
β-strand	315-320	6	1
α-helix	321-330	10
β-strand	335-340	6	6
β-strand	347-351	5	6
β-strand	357-361	5	6
β-strand	364	1	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Beta sliding clamp	A, B	protein	386	Escherichia coli 2-427-07_S4_C3	P0A988 (AlphaFold model)
Peptide 18	H, I	protein	6	synthetic construct

Sequence of entity 1 (A, B), FASTA

>7AZE_1 Beta sliding clamp (chains A, B)
MGSSHHHHHHSSGLVPRGSHMKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADG
TLSLTGTDLEMEMVARVALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVR
SGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLF
ETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGS
NNIRAHVGDFIFTSKLVDGRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRG
VRLYVSENQLKITANNPEQEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMML
TDSVSSVQIEDAASQSAAYVVMPMRL

Sequence of entity 2 (H, I), FASTA

>7AZE_2 Peptide 18 (chains H, I)
XQADLF

Ligands and cofactors

ID	Name	Formula	Copies
MLI	Malonate ion	C3 H2 O4	1

Water and common crystallization additives (GOL, 1PE) are not listed.

Primary citation

Iterative Structure-Based Optimization of Short Peptides Targeting the Bacterial Sliding Clamp. Monsarrat, C., Compain, G., Andre, C. et al. J Med Chem (2021) 64:17063-17078. DOI 10.1021/acs.jmedchem.1c00918 · PubMed

Other PDB entries of the same protein (UniProt P0A988 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8PAY 1.21 Å, Structure of the E.coli DNA polymerase sliding clamp with a covalently bound peptide 2.
8PAT 1.45 Å, Structure of the E.coli DNA polymerase sliding clamp with a covalently bound peptide 3.
4K3L 1.5 Å, E. coli sliding clamp in complex with AcLF dipeptide
8CIY 1.54 Å, DNA-polymerase sliding clamp (DnaN) from Escherichia coli in complex with…
7AZ8 1.61 Å, DNA polymerase sliding clamp from Escherichia coli with peptide 43 bound
4MJR 1.62 Å, E. coli sliding clamp in complex with (S)-Carprofen
6FVM 1.63 Å, Mutant DNA polymerase sliding clamp from Escherichia coli with bound P7 peptide
3D1G 1.64 Å, Structure of a small molecule inhibitor bound to a DNA sliding clamp
1OK7 1.65 Å, A Conserved protein binding-site on Bacterial Sliding Clamps
7AZ7 1.65 Å, DNA polymerase sliding clamp from Escherichia coli with peptide 37 bound
4N96 1.7 Å, E. coli sliding clamp in complex with 6-nitroindazole
4N98 1.7 Å, E. coli sliding clamp in complex with 4'-fluorobiphenyl-4-carboxylic acid

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