6RXM: CobB Ac2

Crystal structure of CobB Ac2 (A76G, I131C, V162G) in complex with H4K16-Acetyl peptide. Determined by X-ray diffraction at 1.92 Å resolution. Released 15 Apr 2020.

Method: X-ray diffraction
Resolution: 1.92 Å
Organisms: Escherichia coli (strain K12), Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 12
Atoms: 12,179
Mol. weight: 176.58 kDa
Ligands: ZN
Released: 15 Apr 2020

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

Secondary structure: helices and β-sheets

6RXM contains 86 α-helices and 89 β-strands across 12 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, 15 β-strands

Element	Residues	Length	Sheet
β-strand	43-47	5	1
α-helix	50-53	4
α-helix	57-59	3
β-strand	63	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
β-strand	252-255	4	1
α-helix	258-271	14

Chain B: 14 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	43-47	5	6
α-helix	49-51	3
α-helix	53-55	3
β-strand	61	1	7
β-strand	66-67	2	7
β-strand	70-71	2	7
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	6
α-helix	134-138	5
β-strand	144-145	2	6
β-strand	148-155	8	8
β-strand	161-163	3	8
β-strand	173	1	9
β-strand	182	1	9
β-strand	183-187	5	8
α-helix	188-189	2
α-helix	193-194	2
α-helix	197-206	10
β-strand	209-213	5	6
β-strand	219-220	2	10
α-helix	222-224	3
α-helix	225-231	7
β-strand	235-240	6	6
β-strand	252-255	4	6
α-helix	258-270	13

Chain C: 14 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	43-47	5	11
α-helix	49-51	3
α-helix	53-55	3
β-strand	61	1	12
β-strand	66-67	2	12
β-strand	70-71	2	12
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	11
α-helix	134-138	5
β-strand	144-145	2	11
β-strand	148-155	8	13
β-strand	161-163	3	13
β-strand	173	1	14
β-strand	182	1	14
β-strand	183-187	5	13
α-helix	188-189	2
α-helix	193-194	2
α-helix	197-206	10
β-strand	209-213	5	11
β-strand	219-220	2	15
α-helix	222-224	3
α-helix	225-231	7
β-strand	235-240	6	11
β-strand	252-255	4	11
α-helix	258-271	14

Chain D: 13 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	43-47	5	16
α-helix	49-55	7
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	16
α-helix	134-138	5
β-strand	144-145	2	16
β-strand	148-155	8	17
β-strand	161-163	3	17
β-strand	173	1	18
β-strand	182	1	18
β-strand	183-187	5	17
α-helix	188-189	2
α-helix	193-194	2
α-helix	197-206	10
β-strand	209-213	5	16
β-strand	219-220	2	19
α-helix	222-224	3
α-helix	225-231	7
β-strand	235-240	6	16
β-strand	252-255	4	16
α-helix	258-271	14

Chain E: 15 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	43-47	5	20
α-helix	49-55	7
α-helix	57-60	4
β-strand	66-67	2	21
β-strand	70-71	2	21
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	20
α-helix	134-138	5
β-strand	144-145	2	20
β-strand	148-155	8	22
β-strand	161-163	3	22
β-strand	173	1	23
β-strand	182	1	23
β-strand	183-187	5	22
α-helix	188-189	2
α-helix	193-194	2
α-helix	197-206	10
β-strand	209-213	5	20
β-strand	219-220	2	24
α-helix	222-224	3
α-helix	225-231	7
β-strand	235-240	6	20
α-helix	247-249	3
β-strand	252-255	4	20
α-helix	258-271	14

Chain F: 15 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	43-47	5	25
α-helix	49-51	3
α-helix	53-55	3
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	25
α-helix	134-138	5
β-strand	144-145	2	25
β-strand	148-155	8	26
β-strand	161-163	3	26
β-strand	173	1	27
β-strand	182	1	27
β-strand	183-187	5	26
α-helix	188-189	2
α-helix	193-194	2
α-helix	197-206	10
β-strand	209-213	5	25
β-strand	219-220	2	28
α-helix	222-224	3
α-helix	225-231	7
β-strand	235-240	6	25
α-helix	247-249	3
β-strand	252-255	4	25
α-helix	258-270	13

Chains G, H, I, J and L: 0 helices, 1 β-strand

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

Chain K: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	17-18	2	24
α-helix	19-20	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NAD-dependent protein deacylase	A, B, C, D, E, F	protein	254	Escherichia coli (strain K12)	P75960 (AlphaFold model)
Histone H4	G, H, I, J, K, L	protein	11	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P02309 (AlphaFold model)

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

>6RXM_1 NAD-dependent protein deacylase (chains A, B, C, D, E, F)
MGSSHHHHHHSQDPKPRVLVLTGAGISAESGIRTFRAADGLWEEHRVEDVGTPEGFDRDP
ELVQAFYNARRRQLQQPEIQPNAAHLALAKLQDALGDRFLLVTQNCDNLHERAGNTNVIH
MHGELLKVRCSQSGQALDWTGDVTPEDKCHCCQFPAPLRPHVVWFGEMPLGMDEIYMALS
MADIFIAIGTSGHVYPAAGFVHEAKLHGAHTVELNLEPSQVGNEFAEKYYGPASQVVPEF
VEKLLKGLKAGSIA

Sequence of entity 2 (G, H, I, J, K, L), FASTA

>6RXM_2 Histone H4 (chains G, H, I, J, K, L)
KGGAKRHRKIL

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	6

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…
6RXJ 1.6 Å, Crystal structure of CobB wt in complex with H4K16-Acetyl peptide
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
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

Browse structure collections

About this viewer

MolViewer shows 6RXM 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.