SAXSdb — 2hke

▼

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

Diphosphomevalonate decarboxylase, putative

Trypanosoma brucei

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 × 3 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	SULFATE ION × 3 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q388P2_9TRYP
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–380； UniProt 1–380 Author chain B； PDBConstruct 1–380； UniProt 1–380

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	2hke
Deposition date deposition_date	2006-07-04
Structure title title	Mevalonate diphosphate decarboxylase from Trypanosoma brucei
Keywords keywords	mevalonate diphosphate decarboxylase, diphosphomevalonate decarboxylase, decarboxylase, LYASE; LYASE
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.

2hke__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2hke__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2hke__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	22.02 Å
Rg (electron density)	21.12 Å
Total Rg	22.01 Å
Atom count	2918
Residues	376
Excluded volume	52317 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2hke__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2hke__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Description description	Diphosphomevalonate decarboxylase, putative
Molecular weight formula_weight	41945.3 kDa
EC 编号 ec_number	4.1.1.33
Mutation mutation	D92E
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	6562

MSDQCVTVEAPINIAFIKYWGKREGGETLILPTNDSFSITLSASPFRSKTSVELRDDIETDTLRLNGTEVDVGKTPRVQSMLLHLRSTCPEELKNKKVNIVSENNFPTAAGMASSASGYCAMSAALIRAFKSTTNVSMLARLGSGSACRSAFGGFVIWNKGEKPDGSDCVATQFVDETHWPEIQVMCAVLKGAQKDVSSTKGMQQSLKTSPLMKKRISETVPERMKIASRAIKARDFATFAEIAMLESDDLQEICATTEPKITYATEDSYAMIRLVKAYNAKKGRTALAYTFDAGANCFLFVLKEDLPEAVAMLMEHFPTPFEKFFFGDRELLEKVKVVSLPDEYKKLIDHPKKPFEMLLQSPVGCGVKYLGPSESLIPP

Source Source

Source organism organism	Trypanosoma brucei
NCBI taxonomy ID ncbi_taxonomy_id	5691
Host organism host_organism	Escherichia coli BL21(DE3)

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	6

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	712

▼

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2hkea1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.14 — Ribosomal protein S5 domain 2-like
Superfamily Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
Family Family family	d.14.1.0 — automated matches

Domain ID domain_id	d2hkea2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.26 — GHMP Kinase, C-terminal domain
Family Family family	d.58.26.0 — automated matches

Domain ID domain_id	d2hkeb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.14 — Ribosomal protein S5 domain 2-like
Superfamily Superfamily superfamily	d.14.1 — Ribosomal protein S5 domain 2-like
Family Family family	d.14.1.0 — automated matches

Domain ID domain_id	d2hkeb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.26 — GHMP Kinase, C-terminal domain
Family Family family	d.58.26.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	2hkeA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2hkeA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	890 — GHMP kinase, C-terminal domain

Domain ID domain_id	2hkeB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2hkeB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	890 — GHMP kinase, C-terminal domain

▶

Unit-cell length a length_a	51.463 Å
Unit-cell length b length_b	168.666 Å
Unit-cell length c length_c	54.850 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	118.78 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	42.180 Å
R factor r_factor	0.1680
R_work r_work	0.1660
R_free r_free	0.2080

Mevalonate diphosphate decarboxylase from Trypanosoma brucei

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

Diphosphomevalonate decarboxylase, putative

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

2hke__assembly_2__model_1

2hke__assembly_2__model_1 | I(q)

2hke__assembly_2__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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (2)

Mevalonate diphosphate decarboxylase from Trypanosoma brucei

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

Diphosphomevalonate decarboxylase, putative

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

2hke__assembly_2__model_1

2hke__assembly_2__model_1 | I(q)

2hke__assembly_2__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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (2)