SAXSdb — 3ham

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

Aminoglycoside phosphotransferase

Enterococcus faecium

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	;(2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL ; × 2 GLYCEROL × 4 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	;(2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL ; × 2 GLYCEROL × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9EVD7_ENTFC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–299； UniProt 1–299 Author chain B； PDBConstruct 1–299； UniProt 1–299

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	3ham
Deposition date deposition_date	2009-05-02
Structure title title	Structure of the gentamicin-APH(2")-IIa complex
Keywords keywords	aminoglycoside, gentamicin, antibiotic resistance, Transferase; TRANSFERASE
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.

3ham__assembly_1__model_1

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

Download this curve (.dat)

3ham__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3ham__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.76 Å
Rg (electron density)	29.38 Å
Total Rg	30.02 Å
Atom count	5064
Residues	598
Excluded volume	90557 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3ham__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3ham__assembly_2__model_1`	dimeric （2）	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 (4)

Entity 1 Entity 1 polymer

Description description	Aminoglycoside phosphotransferase
Molecular weight formula_weight	35398.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5302

MVNLDAEIYEHLNKQIKINELRYLSSGDDSDTFLCNEQYVVKVPKRDSVRISQKREFELYRFLENCKLSYQIPAVVYQSDRFNIMKYIKGERITYEQYHKLSEKEKDALAYDEATFLKELHSIEIDCSVSLFSDALVNKKDKFLQDKKLLISILEKEQLLTDEMLEHIETIYENILNNAVLFKYTPCLVHNDFSANNMIFRNNRLFGVIDFGDFNVGDPDNDFLCLLDCSTDDFGKEFGRKVLKYYQHKAPEVAERKAELNDVYWSIDQIIYGYERKDREMLIKGVSELLQTQAEMFIF

Source Source

Source organism organism	Enterococcus faecium
Common name common_name	Streptococcus faecium
NCBI taxonomy ID ncbi_taxonomy_id	1352
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	;(2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDR OXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL ;
Molecular weight formula_weight	449.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	238

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3hamA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	3hamA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1200 — Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 — Aminoglycoside phosphotransferase (APH), C-terminal lobe

Domain ID domain_id	3hamB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	3hamB02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1200 — Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 — Aminoglycoside phosphotransferase (APH), C-terminal lobe

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Unit-cell length a length_a	79.700 Å
Unit-cell length b length_b	58.800 Å
Unit-cell length c length_c	81.400 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.40 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	35.000 Å
R factor r_factor	0.2132
R_work r_work	0.2100
R_free r_free	0.2710

Structure of the gentamicin-APH(2")-IIa complex

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

Aminoglycoside phosphotransferase

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

3ham__assembly_1__model_1

3ham__assembly_1__model_1 | I(q)

3ham__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Structure of the gentamicin-APH(2")-IIa complex

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

Aminoglycoside phosphotransferase

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

3ham__assembly_1__model_1

3ham__assembly_1__model_1 | I(q)

3ham__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)