SAXSdb — 3irh

▼

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

HD domain protein

Enterococcus faecalis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	CALCIUM ION × 4 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 4 ;2'-DEOXYADENOSINE 5'-TRIPHOSPHATE ; × 2 water × 4	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 ;2'-DEOXYADENOSINE 5'-TRIPHOSPHATE ; × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	CALCIUM ION × 1 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 ;2'-DEOXYADENOSINE 5'-TRIPHOSPHATE ; × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q836G9_ENTFA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 25–480； UniProt 1–456 Author chain B； PDBConstruct 25–480； UniProt 1–456 Author chain C； PDBConstruct 25–480； UniProt 1–456 Author chain D； PDBConstruct 25–480； UniProt 1–456

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	3irh
Deposition date deposition_date	2009-08-24
Structure title title	Structure of an Enterococcus Faecalis HD-domain protein complexed with dGTP and dATP
Keywords keywords	;HD Domain, Phosphohydrolase, dNTPase, Structural Genomics, PSI-2, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, unknown function, HYDROLASE ;; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

3irh__assembly_5__model_1

Assembly 5 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3irh__assembly_5__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3irh__assembly_5__model_1 | P(r) · Pending

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

Rg（Guinier）	25.15 Å
Rg (electron density)	24.58 Å
Total Rg	25.41 Å
Atom count	3611
Residues	434
Excluded volume	63979 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3irh__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3irh__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3irh__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3irh__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3irh__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	HD domain protein
Molecular weight formula_weight	55886.0 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	15380

MHHHHHHSSGVDLGTENLYFQSNAMTIPYKEQRLPIEKVFRDPVHNYIHVQHQVILDLINSAEVQRLRRIKQLGTSSFTFHGAEHSRFSHSLGVYEITRRICEIFQRNYSVERLGENGWNDDERLITLCAALLHDVGHGPYSHTFEHIFDTNHEAITVQIITSPETEVYQILNRVSADFPEKVASVITKQYPNPQVVQMISSQIDADRMDYLLRDAYFTGTEYGTFDLTRILRVIRPYKGGIAFAMNGMHAVEDYIVSRYQMYVQVYFHPVSRGMEVILDHLLHRAKELFENPEFDYDLQASLLVPFFKGDFTLQEYLKLDDGVLSTYFTQWMDVPDSILGDLAKRFLMRKPLKSATFTNEKESAATIAYLRELIEKVGFNPKYYTAINSSYDLPYDFYRPNKDRHRTQIELMQKDGSLVELATVSPLVAALAGQSQGDERFYFPKEMLDQGNKKHYDLFDETYREFSSYIHNGALVLKK

Source Source

Source organism organism	Enterococcus faecalis
Common name common_name	Streptococcus faecalis
NCBI taxonomy ID ncbi_taxonomy_id	226185
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	;2'-DEOXYADENOSINE 5'-TRIPHOSPHATE ;
Molecular weight formula_weight	491.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	409

▼

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3irha_
Class class	a — All alpha proteins
Fold Fold fold	a.211 — HD-domain/PDEase-like
Superfamily Superfamily superfamily	a.211.1 — HD-domain/PDEase-like
Family Family family	a.211.1.1 — HD domain

Domain ID domain_id	d3irhb_
Class class	a — All alpha proteins
Fold Fold fold	a.211 — HD-domain/PDEase-like
Superfamily Superfamily superfamily	a.211.1 — HD-domain/PDEase-like
Family Family family	a.211.1.1 — HD domain

Domain ID domain_id	d3irhc_
Class class	a — All alpha proteins
Fold Fold fold	a.211 — HD-domain/PDEase-like
Superfamily Superfamily superfamily	a.211.1 — HD-domain/PDEase-like
Family Family family	a.211.1.1 — HD domain

Domain ID domain_id	d3irhd_
Class class	a — All alpha proteins
Fold Fold fold	a.211 — HD-domain/PDEase-like
Superfamily Superfamily superfamily	a.211.1 — HD-domain/PDEase-like
Family Family family	a.211.1.1 — HD domain

CATH v4.4 (8 domains)

Domain ID domain_id	3irhA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3210 — Hypothetical protein af1432
Homologous superfamily homologous superfamily	10 — Hypothetical protein af1432

Domain ID domain_id	3irhA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	3irhB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3210 — Hypothetical protein af1432
Homologous superfamily homologous superfamily	10 — Hypothetical protein af1432

Domain ID domain_id	3irhB02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	3irhC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3210 — Hypothetical protein af1432
Homologous superfamily homologous superfamily	10 — Hypothetical protein af1432

Domain ID domain_id	3irhC02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	3irhD01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3210 — Hypothetical protein af1432
Homologous superfamily homologous superfamily	10 — Hypothetical protein af1432

Domain ID domain_id	3irhD02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily	30 —

▶

Unit-cell length a length_a	149.253 Å
Unit-cell length b length_b	188.660 Å
Unit-cell length c length_c	67.822 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	16

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1880
R_work r_work	0.1850
R_free r_free	0.2440

Structure of an Enterococcus Faecalis HD-domain protein complexed with dGTP and dATP

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

HD domain protein

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

3irh__assembly_5__model_1

3irh__assembly_5__model_1 | I(q)

3irh__assembly_5__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Structure of an Enterococcus Faecalis HD-domain protein complexed with dGTP and dATP

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

HD domain protein

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

3irh__assembly_5__model_1

3irh__assembly_5__model_1 | I(q)

3irh__assembly_5__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)