6RXJ: CobB wt

Crystal structure of CobB wt in complex with H4K16-Acetyl peptide. Determined by X-ray diffraction at 1.6 Å resolution. Released 15 Apr 2020.

Method: X-ray diffraction
Resolution: 1.6 Å
Organisms: Escherichia coli (strain K12), Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 4
Atoms: 4,090
Mol. weight: 58.74 kDa
Ligands: ZN
Released: 15 Apr 2020

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

Secondary structure: helices and β-sheets

6RXJ contains 28 α-helices and 32 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.

Chains A and B: 14 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	43-47	5	1
α-helix	49-55	7
β-strand	61	1	2
β-strand	66-67	2	2
β-strand	70-71	2	2
α-helix	72-75	4
α-helix	78-83	6
α-helix	85-99	15
α-helix	108-120	13
α-helix	121-123	3
β-strand	124-128	5	1
α-helix	134-138	5
β-strand	144-145	2	1
β-strand	148-155	8	3
β-strand	161-163	3	3
β-strand	173	1	4
β-strand	182	1	4
β-strand	183-187	5	3
α-helix	188-189	2
α-helix	193-194	2
α-helix	197-206	10
β-strand	209-213	5	1
β-strand	219-220	2	5
α-helix	222-224	3
α-helix	225-231	7
β-strand	235-240	6	1
α-helix	247-249	3
β-strand	252-255	4	1
α-helix	258-272	15

Chains C and D: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	17-18	2	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NAD-dependent protein deacylase	A, B	protein	254	Escherichia coli (strain K12)	P75960 (AlphaFold model)
Histone H4	C, D	protein	10	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P02309 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6RXJ_1 NAD-dependent protein deacylase (chains A, B)
MGSSHHHHHHSQDPKPRVLVLTGAGISAESGIRTFRAADGLWEEHRVEDVATPEGFDRDP
ELVQAFYNARRRQLQQPEIQPNAAHLALAKLQDALGDRFLLVTQNIDNLHERAGNTNVIH
MHGELLKVRCSQSGQVLDWTGDVTPEDKCHCCQFPAPLRPHVVWFGEMPLGMDEIYMALS
MADIFIAIGTSGHVYPAAGFVHEAKLHGAHTVELNLEPSQVGNEFAEKYYGPASQVVPEF
VEKLLKGLKAGSIA

Sequence of entity 2 (C, D), FASTA

>6RXJ_2 Histone H4 (chains C, D)
KGGAKRHRKI

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

Evolved, Selective Erasers of Distinct Lysine Acylations. Spinck, M., Neumann-Staubitz, P., Ecke, M. et al. Angew Chem Int Ed Engl (2020) 59:11142-11149. DOI 10.1002/anie.202002899 · PubMed

Other PDB entries of the same protein (UniProt P75960 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6RXK 1.35 Å, Crystal structure of CobB wt in complex with H4K16-Butyryl peptide
6RXS 1.6 Å, Crystal structure of CobB Ac3(A76G,Y92A, I131L, V187Y) in complex with H4K16-Acetyl…
6RXQ 1.7 Å, Crystal structure of CobB Ac2 (A76G,I131C,V162A) in complex with H4K16Cr-2'OH-ADPr…
6RXR 1.7 Å, Crystal structure of CobB Ac2 (A76G, I131C, V162G) in complex with H4K16Cr-2'OH-ADPr…
6RXP 1.8 Å, Crystal structure of CobB Ac2 (A76G,I131C,V162A) in complex with H4K16-Crotonyl peptide
6RXM 1.92 Å, Crystal structure of CobB Ac2 (A76G, I131C, V162G) in complex with H4K16-Acetyl peptide
6RXO 1.95 Å, Crystal structure of CobB Ac2 (A76G, I131C, V162A) in complex with H4K16-Buturyl peptide
1S5P 1.96 Å, Structure and substrate binding properties of cobB, a Sir2 homolog protein deacetylase…
6RXL 2.3 Å, Crystal structure of CobB wt in complex with H4K16-Crotonyl peptide
8ZSF 3.24 Å, CryoEM Helical Structure of KomC

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