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1dil

SIALIDASE FROM SALMONELLA TYPHIMURIUM COMPLEXED WITH APANA AND EPANA INHIBITORS

Method: X-RAY DIFFRACTION Dmax: 61.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

SIALIDASE

Salmonella typhimurium

UniProt P29768

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–381 Not recorded EQP (1R)-4-acetamido-1,5-anhydro-2,4-dideoxy-1-phosphono-D-glycero-D-galacto-octitol × 1 AXP (1S)-4-acetamido-1,5-anhydro-2,4-dideoxy-1-phosphono-D-glycero-D-galacto-octitol × 1 K POTASSIUM ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 1.90 Å

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.

Other PDB Difference from Current Entry 1DIL Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1DIM SIALIDASE FROM SALMONELLA TYPHIMURIUM COMPLEXED WITH EPANA INHIBITOR Deposited 1996-04-23 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–381（381 aa）
Not recorded K POTASSIUM ION × 1 EQP (1R)-4-acetamido-1,5-anhydro-2,4-dideoxy-1-phosphono-D-glycero-D-galacto-octitol × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.60 Å
2SIL THE STRUCTURES OF SALMONELLA TYPHIMURIUM LT2 NEURAMINIDASE AND ITS COMPLEX WITH A TRANSITION STATE ANALOGUE AT 1.6 ANGSTROMS RESOLUTION Deposited 1994-07-13 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–381（381 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.60 Å
2SIM THE STRUCTURES OF SALMONELLA TYPHIMURIUM LT2 NEURAMINIDASE AND ITS COMPLEX WITH A TRANSITION STATE ANALOGUE AT 1.6 ANGSTROMS RESOLUTION Deposited 1994-07-15 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–381（381 aa）
Not recorded DAN 2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.60 Å
3SIL SIALIDASE FROM SALMONELLA TYPHIMURIUM Deposited 1998-07-07 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 3–381（379 aa）
Mutation：RESIDUE MET 1 WAS EXCISED BY ESCHERICHIA COLI K POTASSIUM ION × 1 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.86；pH 7.86
Resolution 1.05 Å R-free 0.147
6TRG Salmonella typhimurium neuraminidase mutant (D100S) Deposited 2019-12-18 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain XXX 4–382（379 aa）
Mutation：D100S GOL GLYCEROL × 7 PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；Crystals grown by hanging drop vapour diffusion. A 1:1 mixture of 15mg/ml protein solution and an 8:4 mixture of 3.0M K2HPO4 to 1.4M KH2P04 was placed above a well of an 8:6 solution of 3.0M K2HPO4 to 1.4M KH2PO4. Then serially cryoprotected in situ to 40% glycerol (v/v with mother liquor) in 10% increments over a period of a few minutes.
Resolution 1.00 Å R-free 0.116
6TVI Salmonella typhimurium mutant neuraminidase (D100S)+ DANA Deposited 2020-01-09 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain AAA 4–382（379 aa）
Mutation：D100S GOL GLYCEROL × 6 DAN 2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；Crystals grown by hanging drop vapour diffusion. A 1:1 mixture of 15mg/ml protein solution and an 8:4 mixture of 3.0M K2HPO4 to 1.4M KH2P04 was placed above a well of an 8:6 solution of 3.0M K2HPO4 to 1.4M KH2PO4. Then serially cryoprotected in situ to 40% glycerol (v/v with mother liquor) in 10% increments over a period of a few minutes.
Resolution 1.00 Å R-free 0.133
7AEY Salmonella typhimurium neuraminidase in complex with isocarba-DANA. Deposited 2020-09-18 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain AAA 4–382（379 aa）
Not recorded GOL GLYCEROL × 3 R8T (3~{S},4~{S},5~{R})-4-acetamido-3-oxidanyl-5-[(1~{S},2~{R})-1,2,3-tris(oxidanyl)propyl]cyclohexane-1-carboxylic acid × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；Crystals grown by hanging drop vapour diffusion. A 1:1 mixture of protein solution and an 8:4 mixture of K2HPO4 to KH2PO4 was placed above a well of an 8:6 solution of K2HPO4 to KH2PO4. Then serially cryoprotected in situ to 40% glycerol (v/v with mother liquor) in 10% increments over a period of a few minutes. A 2.5mM solution of isocarba-DANA was then soaked into the resultant crystals for 90 minutes at a temperature of 293K.
Resolution 0.92 Å R-free 0.115
7AF2 Salmonella typhimurium neuraminidase mutant (D62G) Deposited 2020-09-19 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain AAA 4–382（379 aa）
Mutation：D62G GOL GLYCEROL × 5 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；Crystals grown by hanging drop vapour diffusion. A 1:1 mixture of protein solution and an 8:4 mixture of K2HPO4 to KH2PO4 was placed above a well of an 8:6 solution of K2HPO4 to KH2PO4. Then serially cryoprotected in situ to 40% glycerol (v/v with mother liquor) in 10% increments over a period of a few minutes.
Resolution 0.79 Å R-free 0.132

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NANH_SALTY
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–381； UniProt 1–381

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 1dil

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1dil
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1dil
Deposition date deposition_date1996-04-23
Structure title titleSIALIDASE FROM SALMONELLA TYPHIMURIUM COMPLEXED WITH APANA AND EPANA INHIBITORS
Keywords keywordsGLYCOSIDASE, HYDROLASE; GLYCOSIDASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier20.35 Å
Radius of gyration Rg (electron density) rg_electron19.27 Å
Forward intensity I(0) i031391100.00
Molecular weight molecular_weight42313.0 kDa
Excluded volume excluded_volume52531 ų
Envelope volume envelope_volume58019 ų
Hydration-shell volume shell_volume24057 ų
Envelope diameter envelope_diameter63.5 Å
Shell Rg shell_rg26.78 Å
Envelope Rg envelope_rg19.49 Å
Shape Rg shape_rg19.26 Å
Total Rg total_rg20.18 Å
Total atoms total_atoms2976
Residues n_residues381
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax61.5 Å
Rg (real space) rg_real20.18 Å
Rg uncertainty (real space) rg_real_error0.28 Å
I(0) (real space) i0_real3.1390e+07
I(0) uncertainty (real space) i0_real_error3.6220e+05
Rg (reciprocal space) rg_reciprocal20.21 Å
I(0) (reciprocal space) i0_reciprocal31390000.0000
Solution quality estimate total_estimate0.8987
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.2 Å
Skewness Skewness skewness0.055
Kurtosis Kurtosis kurtosis-0.485
Angular range angular_range— – 0.3900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7961000.0000
Real-space data points n_real_points71
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.912; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.974
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1dila_
Class classb — All beta proteins
Fold Fold foldb.68 — 6-bladed beta-propeller
Superfamily Superfamily superfamilyb.68.1 — Sialidases
Family Family familyb.68.1.1 — Sialidases (neuraminidases)

CATH v4.4 (1 domains)

Domain ID domain_id1dilA00
Class class2 — Mainly Beta
Architecture architecture120 — 6 Propeller
Topology topology10 — Neuraminidase
Homologous superfamily homologous superfamily10 —
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8. Citations (4)

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9. Files and Curves (10)