3kr4

Structure of a protease 3

Method: X-RAY DIFFRACTION Dmax: 210.9 Å Quality: GOOD

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

M17 leucyl aminopeptidase

Plasmodium falciparum

UniProt Q8IL11

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 84–605 Chain B; UniProt 84–605 Chain C; UniProt 84–605 Chain D; UniProt 84–605 Chain E; UniProt 84–605 Chain F; UniProt 84–605 Fragment:residues 84-605 Mutation:N152Q, N515Q, N546Q CO3 CARBONATE ION × 6 ZN ZINC ION × 6 BES 2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL-PENTANOIC ACID × 6 MG MAGNESIUM ION × 6 SO4 SULFATE ION × 8 1PE PENTAETHYLENE GLYCOL × 17 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;298 K;40% PEG 400, 0.1M Tris pH 8.5, 0.2M LiSo4, 1mM TCEP, 1mM MgCl2, 1mM Bestatin, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.00 Å R-free 0.242
2 Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain G; UniProt 84–605 Chain H; UniProt 84–605 Chain I; UniProt 84–605 Chain J; UniProt 84–605 Chain K; UniProt 84–605 Chain L; UniProt 84–605 Fragment:residues 84-605 Mutation:N152Q, N515Q, N546Q CO3 CARBONATE ION × 6 ZN ZINC ION × 6 BES 2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL-PENTANOIC ACID × 6 MG MAGNESIUM ION × 6 SO4 SULFATE ION × 6 1PE PENTAETHYLENE GLYCOL × 20 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;298 K;40% PEG 400, 0.1M Tris pH 8.5, 0.2M LiSo4, 1mM TCEP, 1mM MgCl2, 1mM Bestatin, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.00 Å R-free 0.242

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

16 other PDB entries and 30 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q8IL11_PLAF7
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–522; UniProt 84–605 Author chain B; PDBConstruct 1–522; UniProt 84–605 Author chain C; PDBConstruct 1–522; UniProt 84–605 Author chain D; PDBConstruct 1–522; UniProt 84–605 Author chain E; PDBConstruct 1–522; UniProt 84–605 Author chain F; PDBConstruct 1–522; UniProt 84–605 Author chain G; PDBConstruct 1–522; UniProt 84–605 Author chain H; PDBConstruct 1–522; UniProt 84–605 Author chain I; PDBConstruct 1–522; UniProt 84–605 Author chain J; PDBConstruct 1–522; UniProt 84–605 Author chain K; PDBConstruct 1–522; UniProt 84–605 Author chain L; PDBConstruct 1–522; UniProt 84–605

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.

SAXS scattering curve SAXS Profile

SAXS profile for 3kr4

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3kr4
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3kr4
Deposition date deposition_date2009-11-17
Structure title titleStructure of a protease 3
Keywords keywordsprotease, Aminopeptidase, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier71.58
Radius of gyration Rg (electron density) rg_electron71.85
Forward intensity I(0) i06062390000.00
Molecular weight molecular_weight684530.0 kDa
Excluded volume excluded_volume865170 ų
Envelope volume envelope_volume1166200 ų
Hydration-shell volume shell_volume133750 ų
Envelope diameter envelope_diameter247.2
Shell Rg shell_rg70.50
Envelope Rg envelope_rg70.57
Shape Rg shape_rg71.87
Total Rg total_rg71.75
Total atoms total_atoms48125
Residues n_residues6168
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax210.9
Rg (real space) rg_real71.47
Rg uncertainty (real space) rg_real_error1.17
I(0) (real space) i0_real6.0450e+09
I(0) uncertainty (real space) i0_real_error1.1990e+08
Rg (reciprocal space) rg_reciprocal70.36
I(0) (reciprocal space) i0_reciprocal6044000000.0000
Solution quality estimate total_estimate0.8063
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary57.5
Skewness Skewness skewness0.387
Kurtosis Kurtosis kurtosis-0.729
Angular range angular_range— – 0.1100 −1
Current regularization parameter α current_alpha0.0202
Highest regularization parameter α highest_alpha1769000000.0000
Real-space data points n_real_points23
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.835; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.001

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (8)

7. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

Domain ID domain_id3kr4A01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily10 — Leucine Aminopeptidase, subunit E, domain 1
Domain ID domain_id3kr4A02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology630 — Aminopeptidase
Homologous superfamily homologous superfamily10 — Zn peptidases
Domain ID domain_id3kr4B01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily10 — Leucine Aminopeptidase, subunit E, domain 1
Domain ID domain_id3kr4B02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology630 — Aminopeptidase
Homologous superfamily homologous superfamily10 — Zn peptidases
Domain ID domain_id3kr4C01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily10 — Leucine Aminopeptidase, subunit E, domain 1
Domain ID domain_id3kr4C02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology630 — Aminopeptidase
Homologous superfamily homologous superfamily10 — Zn peptidases
Domain ID domain_id3kr4D01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily10 — Leucine Aminopeptidase, subunit E, domain 1
Domain ID domain_id3kr4D02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology630 — Aminopeptidase
Homologous superfamily homologous superfamily10 — Zn peptidases
Domain ID domain_id3kr4E01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily10 — Leucine Aminopeptidase, subunit E, domain 1
Domain ID domain_id3kr4E02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology630 — Aminopeptidase
Homologous superfamily homologous superfamily10 — Zn peptidases
Domain ID domain_id3kr4F01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily10 — Leucine Aminopeptidase, subunit E, domain 1
Domain ID domain_id3kr4F02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology630 — Aminopeptidase
Homologous superfamily homologous superfamily10 — Zn peptidases
Domain ID domain_id3kr4G01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily10 — Leucine Aminopeptidase, subunit E, domain 1
Domain ID domain_id3kr4G02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology630 — Aminopeptidase
Homologous superfamily homologous superfamily10 — Zn peptidases
Domain ID domain_id3kr4H01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily10 — Leucine Aminopeptidase, subunit E, domain 1
Domain ID domain_id3kr4H02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology630 — Aminopeptidase
Homologous superfamily homologous superfamily10 — Zn peptidases
Domain ID domain_id3kr4I01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily10 — Leucine Aminopeptidase, subunit E, domain 1
Domain ID domain_id3kr4I02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology630 — Aminopeptidase
Homologous superfamily homologous superfamily10 — Zn peptidases
Domain ID domain_id3kr4J01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily10 — Leucine Aminopeptidase, subunit E, domain 1
Domain ID domain_id3kr4J02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology630 — Aminopeptidase
Homologous superfamily homologous superfamily10 — Zn peptidases
Domain ID domain_id3kr4K01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily10 — Leucine Aminopeptidase, subunit E, domain 1
Domain ID domain_id3kr4K02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology630 — Aminopeptidase
Homologous superfamily homologous superfamily10 — Zn peptidases
Domain ID domain_id3kr4L01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology220 — Leucine Aminopeptidase, subunit E; domain 1
Homologous superfamily homologous superfamily10 — Leucine Aminopeptidase, subunit E, domain 1
Domain ID domain_id3kr4L02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology630 — Aminopeptidase
Homologous superfamily homologous superfamily10 — Zn peptidases

8. Citations (1)

9. Files and Curves (10)