1S5P: NAD-dependent deacetylase

Structure and substrate binding properties of cobB, a Sir2 homolog protein deacetylase from Eschericia coli. Determined by X-ray diffraction at 1.96 Å resolution. Released 23 Mar 2004.

Method: X-ray diffraction
Resolution: 1.96 Å
Organism: Escherichia coli
Chains: 2
Atoms: 2,044
Mol. weight: 27.11 kDa
Ligands: ZN
Released: 23 Mar 2004

Explore 1S5P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1S5P contains 14 α-helices and 15 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: 14 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	43-47	5	1
α-helix	50-53	4
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	183-187	5	3
α-helix	188-189	2
β-strand	190	1	4
β-strand	192	1	4
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
α-helix	234	1
β-strand	235-240	6	1
β-strand	252-255	4	1
α-helix	258-272	15

Chain B: 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 deacetylase	A	protein	235	Escherichia coli	P75960 (AlphaFold model)
Histone H4 (residues 12-19)	B	protein	8

Sequence of entity 1 (A), FASTA

>1S5P_1 NAD-dependent deacetylase (chains A)
KPRVLVLTGAGISAESGIRTFRAADGLWEEHRVEDVATPEGFDRDPELVQAFYNARRRQL
QQPEIQPNAAHLALAKLQDALGDRFLLVTQNIDNLHERAGNTNVIHMHGELLKVRCSQSG
QVLDWTGDVTPEDKCHCCQFPAPLRPHVVWFGEMPLGMDEIYMALSMADIFIAIGTSGHV
YPAAGFVHEAKLHGAHTVELNLEPSQVGNEFAEKYYGPASQVVPEFVEKLLKGLK

Sequence of entity 2 (B), FASTA

>1S5P_2 HISTONE H4 (RESIDUES 12-19) (chains B)
KGGAKRHR

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

Primary citation

Structure and Substrate Binding Properties of cobB, a Sir2 Homolog Protein Deacetylase from Eschericia coli. Zhao, K., Chai, X., Marmorstein, R. J Mol Biol (2004) 337:731-741. DOI 10.1016/j.jmb.2004.01.060 · 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
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
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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