8cfy

Crystal structure of S-adenosyl-L-homocysteine hydrolase from P. aeruginosa in complex with F2X-Entry library fragment H08

Method: X-RAY DIFFRACTION

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

Adenosylhomocysteinase

Pseudomonas aeruginosa PAO1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 8	NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 8 ADENINE × 8 POTASSIUM ION × 8 PHOSPHATE ION × 26 DIMETHYL SULFOXIDE × 6 ~{N}-methyl-~{N}-[(1-methylpyrazol-4-yl)methyl]cyclohexanecarboxamide × 2 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SAHH_PSEAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–472； UniProt 1–469 Author chain B； PDBConstruct 4–472； UniProt 1–469 Author chain C； PDBConstruct 4–472； UniProt 1–469 Author chain D； PDBConstruct 4–472； UniProt 1–469 Author chain G； PDBConstruct 4–472； UniProt 1–469 Author chain H； PDBConstruct 4–472； UniProt 1–469 Author chain I； PDBConstruct 4–472； UniProt 1–469 Author chain J； PDBConstruct 4–472； UniProt 1–469

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8cfy
Deposition date deposition_date	2023-02-03
Last revision last_revision	2024-02-21
Structure title title	Crystal structure of S-adenosyl-L-homocysteine hydrolase from P. aeruginosa in complex with F2X-Entry library fragment H08
Keywords keywords	Fragment screening, protein-ligand complex, drug discovery, SAM-DEPENDENT METHYLATION REACTIONS, SAHase, AHCY, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

8cfy__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

8cfy__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8cfy__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	51.28 Å
Rg (electron density)	51.39 Å
Total Rg	51.40 Å
Atom count	29066
Residues	3692
Excluded volume	516140 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8cfy__assembly_1__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	Adenosylhomocysteinase
Molecular weight formula_weight	51735.0 kDa
EC 编号 ec_number	3.3.1.1
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,G,H,I,J
Atom count atom_count	32191

SNAMSAVMTPAGFTDYKVADITLAAWGRRELIIAESEMPALMGLRRKYAGQQPLKGAKILGCIHMTIQTGVLIETLVALGAEVRWSSCNIFSTQDQAAAAIAAAGIPVFAWKGETEEEYEWCIEQTILKDGQPWDANMVLDDGGDLTEILHKKYPQMLERIHGITEETTTGVHRLLDMLKNGTLKVPAINVNDSVTKSKNDNKYGCRHSLNDAIKRGTDHLLSGKQALVIGYGDVGKGSSQSLRQEGMIVKVAEVDPICAMQACMDGFEVVSPYKNGINDGTEASIDAALLGKIDLIVTTTGNVNVCDANMLKALKKRAVVCNIGHFDNEIDTAFMRKNWAWEEVKPQVHKIHRTGKDGFDAHNDDYLILLAEGRLVNLGNATGHPSRIMDGSFANQVLAQIHLFEQKYADLPAAEKAKRLSVEVLPKKLDEEVALEMVKGFGGVVTQLTPKQAEYIGVSVEGPFKPDTYRY

Source Source

Source organism organism	Pseudomonas aeruginosa PAO1
NCBI taxonomy ID ncbi_taxonomy_id	208964
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Molecular weight formula_weight	663.4 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	ADENINE
Molecular weight formula_weight	135.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 5 Entity 5 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	26

Entity 6 Entity 6 non-polymer

Description description	DIMETHYL SULFOXIDE
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 7 Entity 7 non-polymer

Description description	~{N}-methyl-~{N}-[(1-methylpyrazol-4-yl)methyl]cyclohexanecarboxamide
Molecular weight formula_weight	235.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2903

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Unit-cell length a length_a	109.085 Å
Unit-cell length b length_b	103.191 Å
Unit-cell length c length_c	175.392 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.55 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 1 2 1
Space-group number int_tables_number	3
Crystal system crystal_system	—

Resolution resolution	1.880 Å
Low-resolution limit resolution_low	42.610 Å
R factor r_factor	0.1738
R_work r_work	0.1737
R_free r_free	0.2093

Crystal structure of S-adenosyl-L-homocysteine hydrolase from P. aeruginosa in complex with F2X-Entry library fragment H08

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

Adenosylhomocysteinase

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8cfy__assembly_1__model_1

8cfy__assembly_1__model_1 | I(q)

8cfy__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)

Crystal structure of S-adenosyl-L-homocysteine hydrolase from P. aeruginosa in complex with F2X-Entry library fragment H08

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

Adenosylhomocysteinase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8cfy__assembly_1__model_1

8cfy__assembly_1__model_1 | I(q)

8cfy__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)