5ama

Crystal structure of the Angiotensin-1 converting enzyme N-domain in complex with amyloid-beta 1-16

Method: X-RAY DIFFRACTION Dmax: 165.6 Å Quality: GOOD

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

ANGIOTENSIN-CONVERTING ENZYME

HOMO SAPIENS

UniProt P12821

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Monomer Protein × 1 其他Polymer 2 PDB declaration: monomeric(1) Consistent with protein copy count Chain D; UniProt 30–658 Fragment:N DOMAIN, UNP RESIDUES 30-658 Mutation:YES alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 ASP ASPARTIC ACID × 1 SER SERINE × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PEG DI(HYDROXYETHYL)ETHER × 3 P6G HEXAETHYLENE GLYCOL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:pH 8.5;0.06 M DIVALENT CATIONS, 0.1 M TRIS/BICINE PH 8.5, 30 % PEG550MME/PEG20000 Resolution 1.80 Å R-free 0.218
2 Other combination Monomer Protein × 1 其他Polymer 3 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 30–658 Fragment:N DOMAIN, UNP RESIDUES 30-658 Mutation:YES 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 ASP ASPARTIC ACID × 1 SER SERINE × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 2 P6G HEXAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 8.5;0.06 M DIVALENT CATIONS, 0.1 M TRIS/BICINE PH 8.5, 30 % PEG550MME/PEG20000 Resolution 1.80 Å R-free 0.218
3 Other combination Monomer Protein × 1 其他Polymer 2 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 30–658 Fragment:N DOMAIN, UNP RESIDUES 30-658 Mutation:YES 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ASP ASPARTIC ACID × 1 SER SERINE × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PEG DI(HYDROXYETHYL)ETHER × 3 P6G HEXAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 8.5;0.06 M DIVALENT CATIONS, 0.1 M TRIS/BICINE PH 8.5, 30 % PEG550MME/PEG20000 Resolution 1.80 Å R-free 0.218
4 Other combination Monomer Protein × 1 其他Polymer 3 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 30–658 Fragment:N DOMAIN, UNP RESIDUES 30-658 Mutation:YES 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 ASP ASPARTIC ACID × 1 SER SERINE × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 3 P6G HEXAETHYLENE GLYCOL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:pH 8.5;0.06 M DIVALENT CATIONS, 0.1 M TRIS/BICINE PH 8.5, 30 % PEG550MME/PEG20000 Resolution 1.80 Å R-free 0.218

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.

89 other PDB entries and 147 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ACE_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–629; UniProt 30–658 Author chain B; PDBConstruct 1–629; UniProt 30–658 Author chain C; PDBConstruct 1–629; UniProt 30–658 Author chain D; PDBConstruct 1–629; UniProt 30–658

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 5ama

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5ama
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5ama
Deposition date deposition_date2015-03-10
Structure title titleCrystal structure of the Angiotensin-1 converting enzyme N-domain in complex with amyloid-beta 1-16
Keywords keywordsMETALLOPROTEASE, AMYLOID- BETA, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier50.14
Radius of gyration Rg (electron density) rg_electron49.80
Forward intensity I(0) i01174390000.00
Molecular weight molecular_weight288230.0 kDa
Excluded volume excluded_volume360530 ų
Envelope volume envelope_volume481580 ų
Hydration-shell volume shell_volume78432 ų
Envelope diameter envelope_diameter162.1
Shell Rg shell_rg55.95
Envelope Rg envelope_rg48.62
Shape Rg shape_rg49.79
Total Rg total_rg50.02
Total atoms total_atoms20363
Residues n_residues2424
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 dmax165.6
Rg (real space) rg_real50.08
Rg uncertainty (real space) rg_real_error1.66
I(0) (real space) i0_real1.1740e+09
I(0) uncertainty (real space) i0_real_error2.4280e+07
Rg (reciprocal space) rg_reciprocal50.18
I(0) (reciprocal space) i0_reciprocal1175000000.0000
Solution quality estimate total_estimate0.8898
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary69.5
Skewness Skewness skewness0.170
Kurtosis Kurtosis kurtosis-0.651
Angular range angular_range— – 0.1550 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha327000000.0000
Real-space data points n_real_points32
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.902; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.872

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (14)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd5amaa_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.92 — Zincin-like
Superfamily Superfamily superfamilyd.92.1 — Metalloproteases ('zincins'), catalytic domain
Family Family familyd.92.1.0 — automated matches
Domain ID domain_idd5amab_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.92 — Zincin-like
Superfamily Superfamily superfamilyd.92.1 — Metalloproteases ('zincins'), catalytic domain
Family Family familyd.92.1.0 — automated matches
Domain ID domain_idd5amac_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.92 — Zincin-like
Superfamily Superfamily superfamilyd.92.1 — Metalloproteases ('zincins'), catalytic domain
Family Family familyd.92.1.0 — automated matches
Domain ID domain_idd5amad_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.92 — Zincin-like
Superfamily Superfamily superfamilyd.92.1 — Metalloproteases ('zincins'), catalytic domain
Family Family familyd.92.1.0 — automated matches

8. Citations (1)

9. Files and Curves (10)