1jym

Crystals of Peptide Deformylase from Plasmodium falciparum with Ten Subunits per Asymmetric Unit Reveal Critical Characteristics of the Active Site for Drug Design

Method: X-RAY DIFFRACTION

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

Peptide Deformylase

Plasmodium falciparum

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 10	COBALT (II) ION × 10 water × 10	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 1–175； UniProt 63–239 Author chain B； PDBConstruct 1–175； UniProt 63–239 Author chain C； PDBConstruct 1–175； UniProt 63–239 Author chain D； PDBConstruct 1–175； UniProt 63–239 Author chain E； PDBConstruct 1–175； UniProt 63–239 Author chain F； PDBConstruct 1–175； UniProt 63–239 Author chain G； PDBConstruct 1–175； UniProt 63–239 Author chain H； PDBConstruct 1–175； UniProt 63–239 Author chain I； PDBConstruct 1–175； UniProt 63–239 Author chain J； PDBConstruct 1–175； UniProt 63–239

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	1jym
Deposition date deposition_date	2001-09-12
Structure title title	Crystals of Peptide Deformylase from Plasmodium falciparum with Ten Subunits per Asymmetric Unit Reveal Critical Characteristics of the Active Site for Drug Design
Keywords keywords	PDF, malaria, plasmodium, deformylation, metalloenzyme, 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.

1jym__assembly_1__model_1

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

Download this curve (.dat)

1jym__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1jym__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	51.98 Å
Rg (electron density)	52.54 Å
Total Rg	52.51 Å
Atom count	14407
Residues	1706
Excluded volume	260570 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1jym__assembly_1__model_1`	decameric （10）	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 (3)

Entity 1 Entity 1 polymer

Description description	Peptide Deformylase
Molecular weight formula_weight	21821.8 kDa
EC 编号 ec_number	3.5.1.31
Source method src_method	man
Copy count entity_count	10

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J
Atom count atom_count	14584

DEIKIVKYPDPILRRRSEVTNFDDNLKRVVRKMFDIMYESKGIGLSAPQVNISKRIIVWNALYEKRKEENERIFINPSIVEQSLVKLKLIEGCLSFGIEGKVERPSIVSISYYDINGYKHLKILKGIHSRIFQHEFDHLNGTLFIDKMTQVDKKKVRPKLNELIRDYKATHSEEPLEHHHHHH

Source Source

Source organism organism	Plasmodium falciparum
Common name common_name	malaria parasite P. falciparum
NCBI taxonomy ID ncbi_taxonomy_id	5833
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	10

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	177

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6. Fold Classification (SCOP + CATH) 23 domains

SCOP 2.08 (13 domains)

Domain ID domain_id	d1jyma1
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	d1jyma2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1jymb1
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	d1jymb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1jymc_
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	d1jymd_
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	d1jyme1
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	d1jyme2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1jymf_
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	d1jymg_
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	d1jymh_
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	d1jymi_
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	d1jymj_
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 (10 domains)

Domain ID domain_id	1jymA00
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	1jymB00
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	1jymC00
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	1jymD00
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	1jymE00
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	1jymF00
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	1jymG00
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	1jymH00
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	1jymI00
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	1jymJ00
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	121.263 Å
Unit-cell length b length_b	121.263 Å
Unit-cell length c length_c	177.272 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	40

Space group space_group	P 41
Space-group number int_tables_number	76
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2339
R_work r_work	0.2306
R_free r_free	0.2960

Crystals of Peptide Deformylase from Plasmodium falciparum with Ten Subunits per Asymmetric Unit Reveal Critical Characteristics of the Active Site for Drug Design

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

Peptide 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

1jym__assembly_1__model_1

1jym__assembly_1__model_1 | I(q)

1jym__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 23 domains

SCOP 2.08 (13 domains)

CATH v4.4 (10 domains)

7. Citations (2)

Crystals of Peptide Deformylase from Plasmodium falciparum with Ten Subunits per Asymmetric Unit Reveal Critical Characteristics of the Active Site for Drug Design

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

Peptide 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

1jym__assembly_1__model_1

1jym__assembly_1__model_1 | I(q)

1jym__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 23 domains

SCOP 2.08 (13 domains)

CATH v4.4 (10 domains)

7. Citations (2)