SAXSdb — 1rl4

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

formylmethionine deformylase

Plasmodium falciparum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	COBALT (II) ION × 1 (2R)-2-{[FORMYL(HYDROXY)AMINO]METHYL}HEXANOIC ACID × 1 ;2-{N'-[2-(5-AMINO-1-PHENYLCARBAMOYL-PENTYLCARBAMOYL)-HEXYL]-HYDRAZINOMETHYL}-HEXANOIC ACID(5-AMINO-1-PHENYLCARBAMOYL-PENTYL)-AMIDE ; × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	COBALT (II) ION × 1 (2R)-2-{[FORMYL(HYDROXY)AMINO]METHYL}HEXANOIC ACID × 1 ;2-{N'-[2-(5-AMINO-1-PHENYLCARBAMOYL-PENTYLCARBAMOYL)-HEXYL]-HYDRAZINOMETHYL}-HEXANOIC ACID(5-AMINO-1-PHENYLCARBAMOYL-PENTYL)-AMIDE ; × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8I372_PLAF7
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–180； UniProt 59–236 Author chain B； PDBConstruct 3–180； UniProt 59–236

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	1rl4
Deposition date deposition_date	2003-11-24
Structure title title	Plasmodium falciparum peptide deformylase complex with inhibitor
Keywords keywords	crystal engineering, drug design, malaria, PDF, peptide deformylase, Plasmodium, 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.

1rl4__assembly_1__model_1

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

Download this curve (.dat)

1rl4__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1rl4__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.73 Å
Rg (electron density)	15.77 Å
Total Rg	16.92 Å
Atom count	1333
Residues	154
Excluded volume	24300 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1rl4__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1rl4__assembly_2__model_1`	monomeric （1）	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 (5)

Entity 1 Entity 1 polymer

Description description	formylmethionine deformylase
Molecular weight formula_weight	22271.9 kDa
EC 编号 ec_number	3.5.1.31
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	2822

MSKNEKDEIKIVKYPDPILRRRSEEVTNFDDNLKRVVRKMFDIMYESKGIGLSAPQVNISKRIIVWNALYEKRKEENERIFINPSIVEQSLVKLKLIEGCLSFPGIEGKVERPSIVSISYYDINGYKHLKILKGIHSRIFQHEFDHLNGTLFIDKMTQVDKKKVRPKLNELIRDYKATHSLEHHHHHH

Source Source

Source organism organism	Plasmodium falciparum
NCBI taxonomy ID ncbi_taxonomy_id	36329
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	COBALT (II) ION
Molecular weight formula_weight	58.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	(2R)-2-{[FORMYL(HYDROXY)AMINO]METHYL}HEXANOIC ACID
Molecular weight formula_weight	189.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	;2-{N'-[2-(5-AMINO-1-PHENYLCARBAMOYL-PENTYLCARBAMOYL)-HEXYL]-HYDRAZINOMETHYL}-HEXANOIC ACID(5-AMINO-1-PHENYLCARBAMOYL-PENTYL)-AMIDE ;
Molecular weight formula_weight	695.0 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	139

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1rl4a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.167 — Peptide deformylase
Superfamily Superfamily superfamily	d.167.1 — Peptide deformylase
Family Family family	d.167.1.1 — Peptide deformylase

Domain ID domain_id	d1rl4b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.167 — Peptide deformylase
Superfamily Superfamily superfamily	d.167.1 — Peptide deformylase
Family Family family	d.167.1.1 — Peptide deformylase

CATH v4.4 (2 domains)

Domain ID domain_id	1rl4A00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	45 — Peptide Deformylase
Homologous superfamily homologous superfamily	10 — Peptide deformylase

Domain ID domain_id	1rl4B00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	45 — Peptide Deformylase
Homologous superfamily homologous superfamily	10 — Peptide deformylase

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Unit-cell length a length_a	102.317 Å
Unit-cell length b length_b	102.317 Å
Unit-cell length c length_c	118.339 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 65
Space-group number int_tables_number	170
Crystal system crystal_system	—

Resolution resolution	2.180 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1981
R_work r_work	0.1973
R_free r_free	0.2122

Plasmodium falciparum peptide deformylase complex with inhibitor

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

formylmethionine deformylase

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

1rl4__assembly_1__model_1

1rl4__assembly_1__model_1 | I(q)

1rl4__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 (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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (2)

Plasmodium falciparum peptide deformylase complex with inhibitor

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

formylmethionine deformylase

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

1rl4__assembly_1__model_1

1rl4__assembly_1__model_1 | I(q)

1rl4__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 (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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (2)