4iru

Crystal Structure of lepB GAP core in a transition state mimetic complex with Rab1A and ALF3

Method: X-RAY DIFFRACTION

▼

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

LepB

Legionella pneumophila

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Ras-related protein Rab-1A × 1 （P62820） ACETATE ION × 4 GLYCEROL × 7 POTASSIUM ION × 5 MAGNESIUM ION × 1 GUANOSINE-5'-DIPHOSPHATE × 1 ALUMINUM FLUORIDE × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Ras-related protein Rab-1A × 1 （P62820） ACETATE ION × 8 GLYCEROL × 1 POTASSIUM ION × 1 MAGNESIUM ION × 1 GUANOSINE-5'-DIPHOSPHATE × 1 ALUMINUM FLUORIDE × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Ras-related protein Rab-1A × 1 （P62820） MAGNESIUM ION × 1 GUANOSINE-5'-DIPHOSPHATE × 1 ALUMINUM FLUORIDE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5ZSM7_LEGPH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–299； UniProt 326–623 Author chain C； PDBConstruct 2–299； UniProt 326–623 Author chain E； PDBConstruct 2–299； UniProt 326–623

Ras-related protein Rab-1A

Homo sapiens

UniProt P62820

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	LepB × 1 （Q5ZSM7） ACETATE ION × 4 GLYCEROL × 7 POTASSIUM ION × 5 MAGNESIUM ION × 1 GUANOSINE-5'-DIPHOSPHATE × 1 ALUMINUM FLUORIDE × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	LepB × 1 （Q5ZSM7） ACETATE ION × 8 GLYCEROL × 1 POTASSIUM ION × 1 MAGNESIUM ION × 1 GUANOSINE-5'-DIPHOSPHATE × 1 ALUMINUM FLUORIDE × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	LepB × 1 （Q5ZSM7） MAGNESIUM ION × 1 GUANOSINE-5'-DIPHOSPHATE × 1 ALUMINUM FLUORIDE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RAB1A_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 11–184； UniProt 4–177 Author chain D； PDBConstruct 11–184； UniProt 4–177 Author chain F； PDBConstruct 11–184； UniProt 4–177

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	4iru
Deposition date deposition_date	2013-01-15
Structure title title	Crystal Structure of lepB GAP core in a transition state mimetic complex with Rab1A and ALF3
Keywords keywords	;Arginine finger, Glutamate finger, P-loop motif, Nucleotide binding, Intrinsic GTPase activity, GTP hydrolysis, GTP hydrolysis activator, GTPase activating protein (GAP), Protein transport, HYDROLASE-HYDROLASE complex ;; 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.

4iru__assembly_1__model_1

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

Download this curve (.dat)

4iru__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4iru__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.56 Å
Rg (electron density)	23.83 Å
Total Rg	24.79 Å
Atom count	3823
Residues	460
Excluded volume	68971 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4iru__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4iru__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4iru__assembly_3__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 (9)

Entity 1 Entity 1 polymer

Description description	LepB
Molecular weight formula_weight	33916.3 kDa
EC 编号 ec_number	3.6.5.2
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E
Atom count atom_count	11410

SLKPLTLLMTSSTSFSETINQWADILKTTDMEKFSFDSNPINLLELVKQFNLYVDELAITCEANNVWAKERIDSTPNLFALYDNSGGEAIHGHAFVPYYKESIVLRRLFTVDPNTFNLSRFAAFEGPCQLYCKEHKDSAWVKIQTLLTLGNGIINTLKIIKQAQAFGIDEAVTENLKALKEQFIAFQLAEADIKESLKAPSFAEPLPNKESEFFYPIDEKALAKMNGYQLATICLEELNSPKPSPLIERILSNKKFWKRINSAFESGVFKGRTDDPAGKIAKIREWHQLLQISGKKTAG

Source Source

Source organism organism	Legionella pneumophila
NCBI taxonomy ID ncbi_taxonomy_id	272624
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Ras-related protein Rab-1A
Molecular weight formula_weight	21175.2 kDa
EC 编号 ec_number	3.6.5.2
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

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

MGHHHHHHGSMNPEYDYLFKLLLIGDSGVGKSCLLLRFADDTYTESYISTIGVDFKIRTIELDGKTIKLQIWDTAGQERFRTITSSYYRGAHGIIVVYDVTDQESFNNVKQWLQEIDRYASENVNKLLVGNKCDLTTKKVVDYTTAKEFADSLGIPFLETSAKNATNVEQSFMTMAAEIKKRMG

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	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 5 Entity 5 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 6 Entity 6 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 non-polymer

Description description	GUANOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	443.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 8 Entity 8 non-polymer

Description description	ALUMINUM FLUORIDE
Molecular weight formula_weight	84.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	34

▼

6. Fold Classification (SCOP + CATH) 9 domains

CATH v4.4 (9 domains)

Domain ID domain_id	4iruA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	1700 —

Domain ID domain_id	4iruA02
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	830 —

Domain ID domain_id	4iruB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4iruC01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	1700 —

Domain ID domain_id	4iruC02
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	830 —

Domain ID domain_id	4iruD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	4iruE01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	1700 —

Domain ID domain_id	4iruE02
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	830 —

Domain ID domain_id	4iruF00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

▶

Unit-cell length a length_a	139.404 Å
Unit-cell length b length_b	139.404 Å
Unit-cell length c length_c	384.519 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	48

Space group space_group	I 41 2 2
Space-group number int_tables_number	98
Crystal system crystal_system	—

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	43.010 Å
R factor r_factor	0.2325
R_work r_work	0.2295
R_free r_free	0.2881

Crystal Structure of lepB GAP core in a transition state mimetic complex with Rab1A and ALF3

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

LepB

State in the Current Structure

Other States of the Same Protein in the Database

Ras-related protein Rab-1A

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

4iru__assembly_1__model_1

4iru__assembly_1__model_1 | I(q)

4iru__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 (9)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 9 domains

CATH v4.4 (9 domains)

7. Citations (1)

Crystal Structure of lepB GAP core in a transition state mimetic complex with Rab1A and ALF3

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

LepB

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ras-related protein Rab-1A

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

4iru__assembly_1__model_1

4iru__assembly_1__model_1 | I(q)

4iru__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 (9)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 9 domains

CATH v4.4 (9 domains)

7. Citations (1)