2wdt

Crystal structure of Plasmodium falciparum UCHL3 in complex with the suicide inhibitor UbVME

Method: X-RAY DIFFRACTION

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

UBIQUITIN

HOMO SAPIENS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	UBIQUITIN CARBOXYL-TERMINAL HYDROLASE L3 × 1 CHLORIDE ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	UBIQUITIN CARBOXYL-TERMINAL HYDROLASE L3 × 1 CHLORIDE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	UBIQ_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–75； UniProt 1–75 Author chain D； PDBConstruct 1–75； UniProt 1–75

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	2wdt
Deposition date deposition_date	2009-03-26
Structure title title	Crystal structure of Plasmodium falciparum UCHL3 in complex with the suicide inhibitor UbVME
Keywords keywords	;HYDROLASE-PROTEIN BINDING COMPLEX, ENZYME-LIGAND COMPLEX, UBIQUITIN ISOPEPTIDASE, UCH-L SUPERFAMILY, CYSTEIN PROTEINASE, PEPTIDASE_C12, HYDROLASE ;; HYDROLASE/PROTEIN BINDING
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.

2wdt__assembly_1__model_1

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

Download this curve (.dat)

2wdt__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2wdt__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.90 Å
Rg (electron density)	19.58 Å
Total Rg	20.59 Å
Atom count	2275
Residues	279
Excluded volume	40661 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2wdt__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2wdt__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	UBIQUITIN CARBOXYL-TERMINAL HYDROLASE L3
Molecular weight formula_weight	26930.3 kDa
EC 编号 ec_number	3.4.19.12
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	4755

MAKNDIWTPLESNPDSLYLYSCKLGQSKLKFVDIYGFNNDLLDMIPQPVQAVIFLYPVNDNIVSENNTNDKHNLKENFDNVWFIKQYIPNSCGTIALLHLYGNLRNKFELDKDSVLDDFFNKVNEMSAEKRGQELKNNKSIENLHHEFCGQVENRDDILDVDTHFIVFVQIEGKIIELDGRKDHPTVHCFTNGDNFLYDTGKIIQDKFIEKCKDDLRFSALAVIPNDNFDII

Source Source

Source organism organism	PLASMODIUM FALCIPARUM
Common name common_name	MALARIA PARASITE
NCBI taxonomy ID ncbi_taxonomy_id	5833
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	UBIQUITIN
Molecular weight formula_weight	8618.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGX

Source Source

Source organism organism	HOMO SAPIENS
Common name common_name	HUMAN
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	ESCHERICHIA COLI

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 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	189

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d2wdta_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.3 — Cysteine proteinases
Superfamily Superfamily superfamily	d.3.1 — Cysteine proteinases
Family Family family	d.3.1.0 — automated matches

Domain ID domain_id	d2wdtb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d2wdtb2
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	d2wdtc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.3 — Cysteine proteinases
Superfamily Superfamily superfamily	d.3.1 — Cysteine proteinases
Family Family family	d.3.1.0 — automated matches

Domain ID domain_id	d2wdtd1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.1 — Ubiquitin-like
Family Family family	d.15.1.1 — Ubiquitin-related

Domain ID domain_id	d2wdtd2
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

CATH v4.4 (6 domains)

Domain ID domain_id	2wdtA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	418 — Actin-binding Protein, T-fimbrin; domain 1
Homologous superfamily homologous superfamily	80 — Ubiquitin carboxyl-terminal hydrolase, domain 1

Domain ID domain_id	2wdtA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	420 — Ubiquitin carboxyl-terminal hydrolase, domain 2

Domain ID domain_id	2wdtB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	2wdtC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	418 — Actin-binding Protein, T-fimbrin; domain 1
Homologous superfamily homologous superfamily	80 — Ubiquitin carboxyl-terminal hydrolase, domain 1

Domain ID domain_id	2wdtC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	420 — Ubiquitin carboxyl-terminal hydrolase, domain 2

Domain ID domain_id	2wdtD00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

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Unit-cell length a length_a	134.400 Å
Unit-cell length b length_b	75.300 Å
Unit-cell length c length_c	85.700 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	19.850 Å
R factor r_factor	0.1880
R_work r_work	0.1870
R_free r_free	0.2350

Crystal structure of Plasmodium falciparum UCHL3 in complex with the suicide inhibitor UbVME

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

UBIQUITIN

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

2wdt__assembly_1__model_1

2wdt__assembly_1__model_1 | I(q)

2wdt__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of Plasmodium falciparum UCHL3 in complex with the suicide inhibitor UbVME

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

UBIQUITIN

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

2wdt__assembly_1__model_1

2wdt__assembly_1__model_1 | I(q)

2wdt__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)