SAXSdb — 1s5p

▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

NAD-dependent deacetylase

Escherichia coli

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 40–274	Not recorded	HISTONE H4 (RESIDUES 12-19) × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.96 Å R-free 0.270

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1S5P	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6RXJ Crystal structure of CobB wt in complex with H4K16-Acetyl peptide Deposited 2019-06-08	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 40–254（215 aa） Fragment：H4K16Ac	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；0.1M Bis-Tris, 0.03 M HCl, 22% PEG3350	Resolution 1.60 Å R-free 0.188
6RXJ Crystal structure of CobB wt in complex with H4K16-Acetyl peptide Deposited 2019-06-08	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 40–254（215 aa） Fragment：H4K16Ac	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；0.1M Bis-Tris, 0.03 M HCl, 22% PEG3350	Resolution 1.60 Å R-free 0.188
6RXK Crystal structure of CobB wt in complex with H4K16-Butyryl peptide Deposited 2019-06-08	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 40–279（240 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；22% PEG 3350 0.1M Bis-Tris 0.03 mM HCL	Resolution 1.35 Å R-free 0.188
6RXL Crystal structure of CobB wt in complex with H4K16-Crotonyl peptide Deposited 2019-06-08	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 40–279（240 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；0.1 M Bis-Tris 22% PEG 3350 0.03 M HCl	Resolution 2.30 Å R-free 0.250
6RXM Crystal structure of CobB Ac2 (A76G, I131C, V162G) in complex with H4K16-Acetyl peptide Deposited 2019-06-08	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 40–279（240 aa）	Mutation：A76G, I131C, V162A	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1 M Bis-Tris, 0.03 HCl, 23% PEG3350	Resolution 1.92 Å R-free 0.242
6RXM Crystal structure of CobB Ac2 (A76G, I131C, V162G) in complex with H4K16-Acetyl peptide Deposited 2019-06-08	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 40–279（240 aa）	Mutation：A76G, I131C, V162A	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1 M Bis-Tris, 0.03 HCl, 23% PEG3350	Resolution 1.92 Å R-free 0.242
6RXM Crystal structure of CobB Ac2 (A76G, I131C, V162G) in complex with H4K16-Acetyl peptide Deposited 2019-06-08	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 40–279（240 aa）	Mutation：A76G, I131C, V162A	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1 M Bis-Tris, 0.03 HCl, 23% PEG3350	Resolution 1.92 Å R-free 0.242
6RXM Crystal structure of CobB Ac2 (A76G, I131C, V162G) in complex with H4K16-Acetyl peptide Deposited 2019-06-08	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 40–279（240 aa）	Mutation：A76G, I131C, V162A	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1 M Bis-Tris, 0.03 HCl, 23% PEG3350	Resolution 1.92 Å R-free 0.242
6RXM Crystal structure of CobB Ac2 (A76G, I131C, V162G) in complex with H4K16-Acetyl peptide Deposited 2019-06-08	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 40–279（240 aa）	Mutation：A76G, I131C, V162A	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1 M Bis-Tris, 0.03 HCl, 23% PEG3350	Resolution 1.92 Å R-free 0.242
6RXM Crystal structure of CobB Ac2 (A76G, I131C, V162G) in complex with H4K16-Acetyl peptide Deposited 2019-06-08	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 40–279（240 aa）	Mutation：A76G, I131C, V162A	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1 M Bis-Tris, 0.03 HCl, 23% PEG3350	Resolution 1.92 Å R-free 0.242
6RXO Crystal structure of CobB Ac2 (A76G, I131C, V162A) in complex with H4K16-Buturyl peptide Deposited 2019-06-08	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 40–279（240 aa）	Mutation：A76G, I131C, V162A	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；0.1M Bis-Tris, 0.03 M HCl, 23% PEG3350	Resolution 1.95 Å R-free 0.215
6RXO Crystal structure of CobB Ac2 (A76G, I131C, V162A) in complex with H4K16-Buturyl peptide Deposited 2019-06-08	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 40–279（240 aa）	Mutation：A76G, I131C, V162A	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；0.1M Bis-Tris, 0.03 M HCl, 23% PEG3350	Resolution 1.95 Å R-free 0.215
6RXP Crystal structure of CobB Ac2 (A76G,I131C,V162A) in complex with H4K16-Crotonyl peptide Deposited 2019-06-08	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 40–279（240 aa） Fragment：H4K16Cr	Mutation：A76G,I131C,V162A	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；0.1M Bis-Tris, 0.03 M HCl, 23% PEG3350	Resolution 1.80 Å R-free 0.234
6RXP Crystal structure of CobB Ac2 (A76G,I131C,V162A) in complex with H4K16-Crotonyl peptide Deposited 2019-06-08	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 40–279（240 aa） Fragment：H4K16Cr	Mutation：A76G,I131C,V162A	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；0.1M Bis-Tris, 0.03 M HCl, 23% PEG3350	Resolution 1.80 Å R-free 0.234
6RXQ Crystal structure of CobB Ac2 (A76G,I131C,V162A) in complex with H4K16Cr-2'OH-ADPr peptide intermediate after soaking Deposited 2019-06-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 40–279（240 aa） Fragment：H4K16Cr	Mutation：A76G,I131C,V162A	KMQ [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{S})-4-[(~{E})-but-2-enoxy]-3,5-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1 mM Bis-Tris, 0.03M HCl, 23% PEG3350, soaked 36h with 1 mM NAD+	Resolution 1.70 Å R-free 0.228
6RXQ Crystal structure of CobB Ac2 (A76G,I131C,V162A) in complex with H4K16Cr-2'OH-ADPr peptide intermediate after soaking Deposited 2019-06-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 40–279（240 aa） Fragment：H4K16Cr	Mutation：A76G,I131C,V162A	KMQ [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{S})-4-[(~{E})-but-2-enoxy]-3,5-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1 mM Bis-Tris, 0.03M HCl, 23% PEG3350, soaked 36h with 1 mM NAD+	Resolution 1.70 Å R-free 0.228
6RXQ Crystal structure of CobB Ac2 (A76G,I131C,V162A) in complex with H4K16Cr-2'OH-ADPr peptide intermediate after soaking Deposited 2019-06-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 40–279（240 aa） Fragment：H4K16Cr	Mutation：A76G,I131C,V162A	KMQ [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{S})-4-[(~{E})-but-2-enoxy]-3,5-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1 mM Bis-Tris, 0.03M HCl, 23% PEG3350, soaked 36h with 1 mM NAD+	Resolution 1.70 Å R-free 0.228
6RXQ Crystal structure of CobB Ac2 (A76G,I131C,V162A) in complex with H4K16Cr-2'OH-ADPr peptide intermediate after soaking Deposited 2019-06-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 40–279（240 aa） Fragment：H4K16Cr	Mutation：A76G,I131C,V162A	KMQ [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{S})-4-[(~{E})-but-2-enoxy]-3,5-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1 mM Bis-Tris, 0.03M HCl, 23% PEG3350, soaked 36h with 1 mM NAD+	Resolution 1.70 Å R-free 0.228
6RXR Crystal structure of CobB Ac2 (A76G, I131C, V162G) in complex with H4K16Cr-2'OH-ADPr peptide intermediate after co-crystallisation Deposited 2019-06-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 40–279（240 aa）	Not recorded	KMQ [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{S})-4-[(~{E})-but-2-enoxy]-3,5-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.1 M Bis-Tris, 0.02 M HCl, 22% PEG 3350, 1 mM NAD	Resolution 1.70 Å R-free 0.228
6RXR Crystal structure of CobB Ac2 (A76G, I131C, V162G) in complex with H4K16Cr-2'OH-ADPr peptide intermediate after co-crystallisation Deposited 2019-06-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 40–279（240 aa）	Not recorded	KMQ [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{S})-4-[(~{E})-but-2-enoxy]-3,5-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.1 M Bis-Tris, 0.02 M HCl, 22% PEG 3350, 1 mM NAD	Resolution 1.70 Å R-free 0.228
6RXR Crystal structure of CobB Ac2 (A76G, I131C, V162G) in complex with H4K16Cr-2'OH-ADPr peptide intermediate after co-crystallisation Deposited 2019-06-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 40–279（240 aa）	Not recorded	KMQ [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{S})-4-[(~{E})-but-2-enoxy]-3,5-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.1 M Bis-Tris, 0.02 M HCl, 22% PEG 3350, 1 mM NAD	Resolution 1.70 Å R-free 0.228
6RXR Crystal structure of CobB Ac2 (A76G, I131C, V162G) in complex with H4K16Cr-2'OH-ADPr peptide intermediate after co-crystallisation Deposited 2019-06-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 40–279（240 aa）	Not recorded	KMQ [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{S})-4-[(~{E})-but-2-enoxy]-3,5-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.1 M Bis-Tris, 0.02 M HCl, 22% PEG 3350, 1 mM NAD	Resolution 1.70 Å R-free 0.228
6RXS Crystal structure of CobB Ac3(A76G,Y92A, I131L, V187Y) in complex with H4K16-Acetyl peptide Deposited 2019-06-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 40–279（240 aa）	Mutation：A76G,Y92A, I131L, V187Y	ZN ZINC ION × 1 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；0.1M Bis-Tris, 0.03 M HCl, 23% PEG3350	Resolution 1.60 Å R-free 0.205

9 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NPD_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–235； UniProt 40–274

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1s5p
Deposition date deposition_date	2004-01-21
Structure title title	Structure and substrate binding properties of cobB, a Sir2 homolog protein deacetylase from Eschericia coli.
Keywords keywords	protein deacetylase, Sir2 homologue, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	18.73 Å
Radius of gyration Rg (electron density) rg_electron	17.74 Å
Forward intensity I(0) i0	12249300.00
Molecular weight molecular_weight	25788.0 kDa
Excluded volume excluded_volume	32111 Å³
Envelope volume envelope_volume	36927 Å³
Hydration-shell volume shell_volume	17609 Å³
Envelope diameter envelope_diameter	61.9 Å
Shell Rg shell_rg	23.76 Å
Envelope Rg envelope_rg	17.91 Å
Shape Rg shape_rg	17.69 Å
Total Rg total_rg	18.77 Å
Total atoms total_atoms	1815
Residues n_residues	232
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	61.9 Å
Rg (real space) rg_real	18.66 Å
Rg uncertainty (real space) rg_real_error	0.31 Å
I(0) (real space) i0_real	1.2250e+07
I(0) uncertainty (real space) i0_real_error	1.4220e+05
Rg (reciprocal space) rg_reciprocal	18.67 Å
I(0) (reciprocal space) i0_reciprocal	12250000.0000
Solution quality estimate total_estimate	0.7220
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.9 Å
Skewness Skewness skewness	0.264
Kurtosis Kurtosis kurtosis	-0.290
Angular range angular_range	— – 0.4250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2458000.0000
Real-space data points n_real_points	74
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.816; Stabil: 1.000; Sysdev: 0.313; Positv: 1.000; Valcen: 1.000; Smooth: 0.996

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	NAD-dependent deacetylase
Molecular weight formula_weight	26088.6 kDa
EC 编号 ec_number	3.5.1.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2044

KPRVLVLTGAGISAESGIRTFRAADGLWEEHRVEDVATPEGFDRDPELVQAFYNARRRQLQQPEIQPNAAHLALAKLQDALGDRFLLVTQNIDNLHERAGNTNVIHMHGELLKVRCSQSGQVLDWTGDVTPEDKCHCCQFPAPLRPHVVWFGEMPLGMDEIYMALSMADIFIAIGTSGHVYPAAGFVHEAKLHGAHTVELNLEPSQVGNEFAEKYYGPASQVVPEFVEKLLKGLK

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	HISTONE H4 (RESIDUES 12-19)
Molecular weight formula_weight	955.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

KGGAKRHR

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	229

▼

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1s5pa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.31 — DHS-like NAD/FAD-binding domain
Superfamily Superfamily superfamily	c.31.1 — DHS-like NAD/FAD-binding domain
Family Family family	c.31.1.5 — Sir2 family of transcriptional regulators

CATH v4.4 (2 domains)

Domain ID domain_id	1s5pA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1220 — TPP-binding domain

Domain ID domain_id	1s5pA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1600 — SIR2/SIRT2 'Small Domain'
Homologous superfamily homologous superfamily	10 — SIR2/SIRT2 'Small Domain'

▶

8. Citations (1)

▶

Unit-cell length a length_a	93.911 Å
Unit-cell length b length_b	93.911 Å
Unit-cell length c length_c	61.488 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	1.960 Å
Low-resolution limit resolution_low	29.700 Å
R factor r_factor	0.2340
R_work r_work	0.2340
R_free r_free	0.2700

fit	/app/data/saxs_computation/s5/1s5p/1s5p.fit
pddf	/app/data/pr_computation/s5/1s5p/1s5p.pr.out
profile	/app/data/saxs_computation/s5/1s5p/1s5p.dat

Structure and substrate binding properties of cobB, a Sir2 homolog protein deacetylase from Eschericia coli.

1. Protein Identity and Related Structures Protein Identity & Related Structures

NAD-dependent deacetylase

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)