1z5h

Crystal structures of the Tricorn interacting Factor F3 from Thermoplasma acidophilum

Method: X-RAY DIFFRACTION

▼

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

Tricorn protease interacting factor F3

Thermoplasma acidophilum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	SULFATE ION × 13 ZINC ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	SULFATE ION × 4 ZINC ION × 1 water × 1	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 4	SULFATE ION × 34 ZINC ION × 4 water × 4	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 17 ZINC ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TRF3_THEAC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–780； UniProt 1–780 Author chain B； PDBConstruct 1–780； UniProt 1–780

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	1z5h
Deposition date deposition_date	2005-03-18
Structure title title	Crystal structures of the Tricorn interacting Factor F3 from Thermoplasma acidophilum
Keywords keywords	Zinc aminopeptidase, Gluzicins, Tricorn protease, Superhelix, 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.

1z5h__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1z5h__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1z5h__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	40.86 Å
Rg (electron density)	40.24 Å
Total Rg	40.70 Å
Atom count	12677
Residues	1560
Excluded volume	225180 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1z5h__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1z5h__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1z5h__assembly_3__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1z5h__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Tricorn protease interacting factor F3
Molecular weight formula_weight	89492.7 kDa
EC 编号 ec_number	3.4.11.-
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	13456

MEVEKYDLTLDFDIQKRTFNGTETITADAGDIVLDAVGLQINWMKVNGRDTAFTYDGQTVRAPGDSQPQKIEISFAGKVSDSLSGIYYAGRENGMITTHFEATDARRMFPCVDHPAYKAVFAITVVIDKDYDAISNMPPKRIEVSERKVVEFQDTPRMSTYLLYVGIGKFRYEYEKYRDIDLILASLKDIRSKYPLDMARKSVEFYENYFGIPYALPKMHLISVPEFGAGAMENWGAITFREIYMDIAENSAVTVKRNSANVIAHEIAHQWFGDLVTMKWWNDLWLNESFATFMSYKTMDTLFPEWSFWGDFFVSRTSGALRSDSLKNTHPIEVDVRDPDEISQIFDEISYGKGASILRMIEDYAGYEEFRKGISKYLNDHKFGNAEGSDLWTAIEDVSGKPVKRVMEYWIKNPGYPVIKLKRNGRKITMYQTRFLLNGEEEGRWPVPVNIKKKDGVERILLEDEASIEADGLIKINADSAGFYRVLYDDATFSDVMGHYRDLSPLDRIGLVDDLFAFLLSGHIDPETYRQRIRNFFDDEDHNVITAIVGQMEYLRMLTHAFDDDARAFCRSRMQFLTGKQDENLKIALGRVSRLYVMVDESYAEEMSKLFKDFDSAEPEMRSSIATAYALVTGDLKGLLEKFRSVDRDEDRVRIISAFGKLKSNTDLSTVYGMVEKTEIKKQDMISFFSSALETLPGREFIFANLDRIIRLVIRYFTGNRTASRTVEMMIPVIGLDHPDAEDIVRNIGSKNISMGLAKGIEMLAVNRKLVERIRQTAVK

Source Source

Source organism organism	Thermoplasma acidophilum
NCBI taxonomy ID ncbi_taxonomy_id	2303
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	17

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	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	779

▼

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1z5ha1
Class class	b — All beta proteins
Fold Fold fold	b.98 — Zn aminopeptidase N-terminal domain
Superfamily Superfamily superfamily	b.98.1 — Zn aminopeptidase N-terminal domain
Family Family family	b.98.1.1 — Zn aminopeptidase N-terminal domain

Domain ID domain_id	d1z5ha2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.92 — Zincin-like
Superfamily Superfamily superfamily	d.92.1 — Metalloproteases ('zincins'), catalytic domain
Family Family family	d.92.1.13 — Zn aminopeptidase catalytic domain

Domain ID domain_id	d1z5ha3
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.30 — Zn aminopeptidase insert domain
Family Family family	b.1.30.1 — Zn aminopeptidase insert domain

Domain ID domain_id	d1z5ha4
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.1 — ARM repeat
Family Family family	a.118.1.26 — ERAP1 C-terminal-like

Domain ID domain_id	d1z5hb1
Class class	b — All beta proteins
Fold Fold fold	b.98 — Zn aminopeptidase N-terminal domain
Superfamily Superfamily superfamily	b.98.1 — Zn aminopeptidase N-terminal domain
Family Family family	b.98.1.1 — Zn aminopeptidase N-terminal domain

Domain ID domain_id	d1z5hb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.92 — Zincin-like
Superfamily Superfamily superfamily	d.92.1 — Metalloproteases ('zincins'), catalytic domain
Family Family family	d.92.1.13 — Zn aminopeptidase catalytic domain

Domain ID domain_id	d1z5hb3
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.30 — Zn aminopeptidase insert domain
Family Family family	b.1.30.1 — Zn aminopeptidase insert domain

Domain ID domain_id	d1z5hb4
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.1 — ARM repeat
Family Family family	a.118.1.26 — ERAP1 C-terminal-like

CATH v4.4 (6 domains)

Domain ID domain_id	1z5hA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1730 — tricorn interacting facor f3 domain

Domain ID domain_id	1z5hA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	390 — Neutral Protease; domain 2
Homologous superfamily homologous superfamily	10 — Neutral Protease Domain 2

Domain ID domain_id	1z5hA03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1910 —

Domain ID domain_id	1z5hB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1730 — tricorn interacting facor f3 domain

Domain ID domain_id	1z5hB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	390 — Neutral Protease; domain 2
Homologous superfamily homologous superfamily	10 — Neutral Protease Domain 2

Domain ID domain_id	1z5hB03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1910 —

▶

Unit-cell length a length_a	115.200 Å
Unit-cell length b length_b	183.300 Å
Unit-cell length c length_c	105.600 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 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	19.480 Å
R factor r_factor	0.2250
R_work r_work	0.2250
R_free r_free	0.2700

Crystal structures of the Tricorn interacting Factor F3 from Thermoplasma acidophilum

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

Tricorn protease interacting factor F3

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

1z5h__assembly_4__model_1

1z5h__assembly_4__model_1 | I(q)

1z5h__assembly_4__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) 14 domains

SCOP 2.08 (8 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structures of the Tricorn interacting Factor F3 from Thermoplasma acidophilum

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

Tricorn protease interacting factor F3

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

1z5h__assembly_4__model_1

1z5h__assembly_4__model_1 | I(q)

1z5h__assembly_4__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) 14 domains

SCOP 2.08 (8 domains)

CATH v4.4 (6 domains)

7. Citations (1)