6FVM: Beta sliding clamp

Mutant DNA polymerase sliding clamp from Escherichia coli with bound P7 peptide. Determined by X-ray diffraction at 1.63 Å resolution. Released 10 Apr 2019.

Method: X-ray diffraction
Resolution: 1.63 Å
Organisms: Escherichia coli O157:H7, synthetic construct
Chains: 4
Atoms: 6,425
Mol. weight: 85.41 kDa
Ligands: CA
Released: 10 Apr 2019

Explore 6FVM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6FVM contains 27 α-helices and 53 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: 13 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	1
α-helix	7-18	12
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
β-strand	124-131	8	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	197-206	10
β-strand	213-219	7	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	260-272	13
β-strand	280-286	7	4
β-strand	289-295	7	4
β-strand	301-307	7	4
β-strand	309-311	3	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	357-361	5	3
β-strand	364	1	4

Chain B: 14 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	4
α-helix	7-17	11
α-helix	28-31	4
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
β-strand	124-131	8	5
α-helix	132-142	11
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
β-strand	213-219	7	5
β-strand	222-227	6	5
β-strand	230-235	6	5
α-helix	236-237	2
α-helix	240-242	3
α-helix	244-246	3
β-strand	254-259	6	6
α-helix	260-272	13
β-strand	280-286	7	1
β-strand	289-295	7	1
β-strand	301-307	7	1
β-strand	309-310	2	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	368	Escherichia coli O157:H7	P0A988 (AlphaFold model)
P7 peptide	H, I	protein	6	synthetic construct

Sequence of entity 1 (A, B), FASTA

>6FVM_1 Beta sliding clamp (chains A, B)
SHMKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVA
LVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPN
LDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLA
VCSMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVD
GRFPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPE
QEEAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSPVQIEDAASQSAA
YVVMPMRL

Sequence of entity 2 (H, I), FASTA

>6FVM_2 P7 peptide (chains H, I)
XQADLF

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1

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

Primary citation

Peptide Interactions on Bacterial Sliding Clamps. Andre, C., Martiel, I., Wolff, P. et al. ACS Infect Dis (2019). DOI 10.1021/acsinfecdis.9b00089 · 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
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
4MJQ 1.73 Å, E. coli sliding clamp in complex with Bromfenac

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