3kqz

Structure of a protease 2

Method: X-RAY DIFFRACTION Dmax: 215.2 Å Quality: REASONABLE

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 × 12 SO4 SULFATE ION × 16 1PE PENTAETHYLENE GLYCOL × 24 2PE NONAETHYLENE GLYCOL × 2 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 ZnCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.39 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 × 12 SO4 SULFATE ION × 11 1PE PENTAETHYLENE GLYCOL × 29 2PE NONAETHYLENE GLYCOL × 1 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 ZnCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.39 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 3kqz

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id3kqz
Deposition date deposition_date2009-11-17
Structure title titleStructure of a protease 2
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_guinier69.38
Radius of gyration Rg (electron density) rg_electron69.61
Forward intensity I(0) i05993060000.00
Molecular weight molecular_weight676870.0 kDa
Excluded volume excluded_volume853820 ų
Envelope volume envelope_volume1124000 ų
Hydration-shell volume shell_volume133100 ų
Envelope diameter envelope_diameter239.3
Shell Rg shell_rg69.00
Envelope Rg envelope_rg68.48
Shape Rg shape_rg69.64
Total Rg total_rg69.48
Total atoms total_atoms47539
Residues n_residues6145
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 dmax215.2
Rg (real space) rg_real69.57
Rg uncertainty (real space) rg_real_error1.38
I(0) (real space) i0_real5.9900e+09
I(0) uncertainty (real space) i0_real_error1.0750e+08
Rg (reciprocal space) rg_reciprocal68.36
I(0) (reciprocal space) i0_reciprocal5978000000.0000
Solution quality estimate total_estimate0.5730
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary56.1
Skewness Skewness skewness0.412
Kurtosis Kurtosis kurtosis-0.653
Angular range angular_range— – 0.1150 −1
Current regularization parameter α current_alpha0.0102
Highest regularization parameter α highest_alpha1750000000.0000
Real-space data points n_real_points24
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.812; Stabil: 1.000; Sysdev: 0.002; Positv: 1.000; Valcen: 0.988; Smooth: 0.014

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

Domain ID domain_id3kqzA01
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_id3kqzA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology630 — Aminopeptidase
Homologous superfamily homologous superfamily10 — Zn peptidases
Domain ID domain_id3kqzB01
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_id3kqzB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology630 — Aminopeptidase
Homologous superfamily homologous superfamily10 — Zn peptidases
Domain ID domain_id3kqzC01
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_id3kqzC02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology630 — Aminopeptidase
Homologous superfamily homologous superfamily10 — Zn peptidases
Domain ID domain_id3kqzD01
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_id3kqzD02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology630 — Aminopeptidase
Homologous superfamily homologous superfamily10 — Zn peptidases
Domain ID domain_id3kqzE01
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_id3kqzE02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology630 — Aminopeptidase
Homologous superfamily homologous superfamily10 — Zn peptidases
Domain ID domain_id3kqzF01
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_id3kqzF02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology630 — Aminopeptidase
Homologous superfamily homologous superfamily10 — Zn peptidases
Domain ID domain_id3kqzG01
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_id3kqzG02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology630 — Aminopeptidase
Homologous superfamily homologous superfamily10 — Zn peptidases
Domain ID domain_id3kqzH01
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_id3kqzH02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology630 — Aminopeptidase
Homologous superfamily homologous superfamily10 — Zn peptidases
Domain ID domain_id3kqzI01
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_id3kqzI02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology630 — Aminopeptidase
Homologous superfamily homologous superfamily10 — Zn peptidases
Domain ID domain_id3kqzJ01
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_id3kqzJ02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology630 — Aminopeptidase
Homologous superfamily homologous superfamily10 — Zn peptidases
Domain ID domain_id3kqzK01
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_id3kqzK02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology630 — Aminopeptidase
Homologous superfamily homologous superfamily10 — Zn peptidases
Domain ID domain_id3kqzL01
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_id3kqzL02
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)