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5mun

Structural insight into zymogenic latency of gingipain K from Porphyromonas gingivalis.

Method: X-RAY DIFFRACTION Dmax: 79.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Lys-gingipain W83

Porphyromonas gingivalis

UniProt Q51817

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 20–228 Chain B； UniProt 20–228 Fragment：UNP residues 20-228 AZI AZIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；293.15 K；14 % polyvinylpyrrolidone K15 0.1 M Bis-Tris, pH 5.5 Resolution 1.80 Å R-free 0.240

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 5MUN Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4ITC Crystal Structure Analysis of the K1 Cleaved Adhesin domain of Lys-gingipain (Kgp) from Porphyromonas gingivalis W83 Deposited 2013-01-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 982–1154（173 aa） Fragment：K1 Cleaved Adhesin Domain, residues 982-1154
Not recorded CA CALCIUM ION × 2 GAI GUANIDINE × 3 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；298 K；40 mM KH2PO4, 20% (v/v) glycerol, 16% (w/v) PEG 8000, 1 M guanidine hydrochloride, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.55 Å R-free 0.181
4RBM Porphyromonas gingivalis gingipain K (Kgp) catalytic and immunoglobulin superfamily-like domains Deposited 2014-09-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 229–683（455 aa） Fragment：UNP residues 229-683
Not recorded CA CALCIUM ION × 2 NA SODIUM ION × 3 NI NICKEL (II) ION × 1 HIS HISTIDINE × 1 ACT ACETATE ION × 2 AZI AZIDE ION × 3 GOL GLYCEROL × 4 CKC (3S)-3,7-diaminoheptan-2-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；The best crystals were obtained at 20C with protein solution (at 5.7mg/mL in 5mM Tris HCl, pH 7.4, 0.02% sodium azide) and 22% polyethylene glycol 8000, 0.1M sodium cacodylate, pH 6.5, 0.2M calcium acetate as reservoir solution from 2:1 uL drops, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.75 Å R-free 0.172
4TKX Structure of Protease Deposited 2014-05-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain L 229–680（452 aa） Fragment：Catalytic domain
Not recorded SO4 SULFATE ION × 4 NA SODIUM ION × 2 K POTASSIUM ION × 1 ACT ACETATE ION × 1 EDO 1,2-ETHANEDIOL × 10 PB LEAD (II) ION × 1 TCK N-[(1S)-5-amino-1-(chloroacetyl)pentyl]-4-methylbenzenesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；PEG 4000, Sodium Acetate, Ammonium Sulphate
Resolution 1.60 Å R-free 0.145
6I9A Porphyromonas gingivalis gingipain K (Kgp) in complex with inhibitor KYT-36 Deposited 2018-11-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 229–683（455 aa）
Not recorded UNX UNKNOWN LIGAND × 2 NA SODIUM ION × 2 CA CALCIUM ION × 2 H8E benzyl-N-[(2S)-1-[[(3S)-7-amino-1-(benzylamino)-1,2-dioxoheptan-3-yl]amino]-5-(2-methyl-2-phenylhydrazinyl)-1,5-dioxopentan-2-yl]carbamate × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% PEG 8000, 0.1 M HEPES, pH 7.5
Resolution 1.20 Å R-free 0.148
6I9A Porphyromonas gingivalis gingipain K (Kgp) in complex with inhibitor KYT-36 Deposited 2018-11-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 229–683（455 aa）
Not recorded UNX UNKNOWN LIGAND × 2 NA SODIUM ION × 2 CA CALCIUM ION × 2 H8E benzyl-N-[(2S)-1-[[(3S)-7-amino-1-(benzylamino)-1,2-dioxoheptan-3-yl]amino]-5-(2-methyl-2-phenylhydrazinyl)-1,5-dioxopentan-2-yl]carbamate × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 GOL GLYCEROL × 3 DTV (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% PEG 8000, 0.1 M HEPES, pH 7.5
Resolution 1.20 Å R-free 0.148

4 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KGP83_PORGN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 6–214； UniProt 20–228 Author chain B； PDBConstruct 6–214； UniProt 20–228

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 5mun

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id5mun
Deposition date deposition_date2017-01-13
Structure title titleStructural insight into zymogenic latency of gingipain K from Porphyromonas gingivalis.
Keywords keywordsCysteine protease, zymogenic latency, 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_guinier24.76 Å
Radius of gyration Rg (electron density) rg_electron24.07 Å
Forward intensity I(0) i025850600.00
Molecular weight molecular_weight38994.0 kDa
Excluded volume excluded_volume49060 ų
Envelope volume envelope_volume63731 ų
Hydration-shell volume shell_volume23507 ų
Envelope diameter envelope_diameter83.1 Å
Shell Rg shell_rg30.28 Å
Envelope Rg envelope_rg24.09 Å
Shape Rg shape_rg24.09 Å
Total Rg total_rg24.85 Å
Total atoms total_atoms2745
Residues n_residues359
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 dmax79.9 Å
Rg (real space) rg_real24.93 Å
Rg uncertainty (real space) rg_real_error0.54 Å
I(0) (real space) i0_real2.5850e+07
I(0) uncertainty (real space) i0_real_error3.4330e+05
Rg (reciprocal space) rg_reciprocal24.89 Å
I(0) (reciprocal space) i0_reciprocal25850000.0000
Solution quality estimate total_estimate0.8684
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.6 Å
Skewness Skewness skewness0.530
Kurtosis Kurtosis kurtosis-0.191
Angular range angular_range— – 0.3200 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4200000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.840; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.938; Smooth: 0.826
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)