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6dwq

Subtilisin serine protease modified with the protease inhibitor cyanobenzylsulfonylfluoride

Method: X-RAY DIFFRACTION Dmax: 53.4 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

KerA

OrganismNot specified

UniProt Q9FDF2

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 37–310 Fragment：residues 37-310 Non-standard monomer：Yes (specific site not provided by mmCIF) EDO 1,2-ETHANEDIOL × 12 NO3 NITRATE ION × 2 CA CALCIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；298 K；26% PEG 3350, 0.350 M NH4NO3 Resolution 1.27 Å R-free 0.148

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 6DWQ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4GI3 Crystal structure of Greglin in complex with subtilisin Deposited 2012-08-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 37–310（274 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.68M sodium citrate, 0.36M sodium formate, 0.066M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.75 Å R-free 0.201
4HX2 Crystal structure of Streptomyces caespitosus sermetstatin in complex with Bacillus licheniformis subtilisin Deposited 2012-11-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 37–310（274 aa） Fragment：Mature protease
Chain C 37–310（274 aa） Fragment：Mature protease
Not recorded CA CALCIUM ION × 4 ZN ZINC ION × 2 CL CHLORIDE ION × 1 1AX (2R,2'R)-3,3'-oxydipropane-1,2-diol × 1 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 2 IPA ISOPROPYL ALCOHOL × 3 K POTASSIUM ION × 2 CAC CACODYLATE ION × 1 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；0.1 M cacodylate, 0.2 M zinc acetate dihydrate, 10% (v/v) 2-propanol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.25 Å R-free 0.217

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q9FDF2_BACLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–274； UniProt 37–310

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 6dwq

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6dwq
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6dwq
Deposition date deposition_date2018-06-27
Structure title titleSubtilisin serine protease modified with the protease inhibitor cyanobenzylsulfonylfluoride
Keywords keywordsserine protease, subtilisin, HYDROLASE; HYDROLASE
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_guinier17.93 Å
Radius of gyration Rg (electron density) rg_electron16.64 Å
Forward intensity I(0) i015397400.00
Molecular weight molecular_weight28484.0 kDa
Excluded volume excluded_volume35175 ų
Envelope volume envelope_volume38085 ų
Hydration-shell volume shell_volume18532 ų
Envelope diameter envelope_diameter54.5 Å
Shell Rg shell_rg23.45 Å
Envelope Rg envelope_rg16.93 Å
Shape Rg shape_rg16.63 Å
Total Rg total_rg17.62 Å
Total atoms total_atoms3947
Residues n_residues272
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 dmax53.4 Å
Rg (real space) rg_real17.76 Å
Rg uncertainty (real space) rg_real_error0.23 Å
I(0) (real space) i0_real1.5400e+07
I(0) uncertainty (real space) i0_real_error1.9470e+05
Rg (reciprocal space) rg_reciprocal17.78 Å
I(0) (reciprocal space) i0_reciprocal15400000.0000
Solution quality estimate total_estimate0.9034
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary51.9 Å
Skewness Skewness skewness0.027
Kurtosis Kurtosis kurtosis-0.523
Angular range angular_range— – 0.4450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4623000.0000
Real-space data points n_real_points75
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.927; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.988
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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_idd6dwqa_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.41 — Subtilisin-like
Superfamily Superfamily superfamilyc.41.1 — Subtilisin-like
Family Family familyc.41.1.1 — Subtilases

CATH v4.4 (1 domains)

Domain ID domain_id6dwqA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily200 — Peptidase S8/S53 domain
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8. Citations (1)

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9. Files and Curves (10)