4tkx

Structure of Protease

Method: X-RAY DIFFRACTION D_max: 74.7 Å Quality: GOOD

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

Lys-gingipain W83

Porphyromonas gingivalis

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 L； UniProt 229–680	Fragment：Catalytic domain	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

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 4TKX	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 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 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
5MUN Structural insight into zymogenic latency of gingipain K from Porphyromonas gingivalis. Deposited 2017-01-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 20–228（209 aa） Fragment：UNP residues 20-228 Chain B 20–228（209 aa） Fragment：UNP residues 20-228	Not recorded	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
6I9A Porphyromonas gingivalis gingipain K (Kgp) in complex with inhibitor KYT-36 Deposited 2018-11-22	Different construct 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 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 L； PDBConstruct 1–452； UniProt 229–680

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4tkx
Deposition date deposition_date	2014-05-28
Structure title title	Structure of Protease
Keywords keywords	Cysteine protease, Gingivalis, Kgp, co-valent inhibitor, Hydrolase-Hydrolase Inhibitor complex; Hydrolase/Hydrolase Inhibitor
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	22.48 Å
Radius of gyration Rg (electron density) rg_electron	21.42 Å
Forward intensity I(0) i0	43487400.00
Molecular weight molecular_weight	51503.0 kDa
Excluded volume excluded_volume	64235 Å³
Envelope volume envelope_volume	71184 Å³
Hydration-shell volume shell_volume	26973 Å³
Envelope diameter envelope_diameter	75.5 Å
Shell Rg shell_rg	29.07 Å
Envelope Rg envelope_rg	21.72 Å
Shape Rg shape_rg	21.39 Å
Total Rg total_rg	22.35 Å
Total atoms total_atoms	7070
Residues n_residues	452
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	74.7 Å
Rg (real space) rg_real	22.37 Å
Rg uncertainty (real space) rg_real_error	0.43 Å
I(0) (real space) i0_real	4.3490e+07
I(0) uncertainty (real space) i0_real_error	5.6110e+05
Rg (reciprocal space) rg_reciprocal	22.40 Å
I(0) (reciprocal space) i0_reciprocal	43490000.0000
Solution quality estimate total_estimate	0.8771
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.3 Å
Skewness Skewness skewness	0.235
Kurtosis Kurtosis kurtosis	-0.264
Angular range angular_range	— – 0.3550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9974000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.801; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.997

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	Lys-gingipain W83
Molecular weight formula_weight	49900.6 kDa
EC 编号 ec_number	3.4.22.47
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L
Atom count atom_count	7693

DVYTDHGDLYNTPVRMLVVAGAKFKEALKPWLTWKAQKGFYLDVHYTDEAEVGTTNASIKAFIHKKYNDGLAASAAPVFLALVGDTDVISGEKGKKTKKVTDLYYSAVDGDYFPEMYTFRMSASSPEELTNIIDKVLMYEKATMPDKSYLEKVLLIAGADYSWNSQVGQPTIKYGMQYYYNQEHGYTDVYNYLKAPYTGCYSHLNTGVSFANYTAHGSETAWADPLLTTSQLKALTNKDKYFLAIGNCCITAQFDYVQPCFGEVITRVKEKGAYAYIGSSPNSYWGEDYYWSVGANAVFGVQPTFEGTSMGSYDATFLEDSYNTVNSIMWAGNLAATHAGNIGNITHIGAHYYWEAYHVLGDGSVMPYRAMPKTNTYTLPASLPQNQASYSIQASAGSYVAISKDGVLYGTGVANASGVATVSMTKQITENGNYDVVITRSNYLPVIKQIQV

来源 Source

来源生物 organism	Porphyromonas gingivalis
NCBI Class编号 ncbi_taxonomy_id	837
宿主生物 host_organism	Porphyromonas gingivalis

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 7 Entity 7 non-polymer

Description description	LEAD (II) ION
Molecular weight formula_weight	207.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	N-[(1S)-5-amino-1-(chloroacetyl)pentyl]-4-methylbenzenesulfonamide
Molecular weight formula_weight	332.8 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	479

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8. Citations (1)

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Unit-cell length a length_a	116.941 Å
Unit-cell length b length_b	116.941 Å
Unit-cell length c length_c	86.852 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	40.710 Å
R factor r_factor	0.1220
R_work r_work	0.1200
R_free r_free	0.1450

fit	/app/data/saxs_computation/tk/4tkx/4tkx.fit
pddf	/app/data/pr_computation/tk/4tkx/4tkx.pr.out
profile	/app/data/saxs_computation/tk/4tkx/4tkx.dat