6i9a

Porphyromonas gingivalis gingipain K (Kgp) in complex with inhibitor KYT-36

Method: X-RAY DIFFRACTION

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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	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	UNKNOWN ATOM OR ION × 2 SODIUM ION × 2 CALCIUM ION × 2 ;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 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 GLYCEROL × 3 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	UNKNOWN ATOM OR ION × 2 SODIUM ION × 2 CALCIUM ION × 2 ;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 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 GLYCEROL × 3 (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KGP83_PORGN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–455； UniProt 229–683 Author chain B； PDBConstruct 1–455； UniProt 229–683

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6i9a
Deposition date deposition_date	2018-11-22
Structure title title	Porphyromonas gingivalis gingipain K (Kgp) in complex with inhibitor KYT-36
Keywords keywords	peptidase inhibitor, custeine peptidase, gingipain, periodontopathogen, periodontal disease, Porphyromonas gingivalis, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6i9a__assembly_1__model_1`	monomeric （1）	Excluded	—	—
	Exclusion reason： The source record does not identify the atom or ion element unambiguously, so a reliable calculation is not possible.
2	1	`6i9a__assembly_2__model_1`	monomeric （1）	Excluded	—	—
	Exclusion reason： The source record does not identify the atom or ion element unambiguously, so a reliable calculation is not possible.

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	Lys-gingipain W83
Molecular weight formula_weight	51012.8 kDa
EC 编号 ec_number	3.4.22.47
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	9311

DVYTDHGDLYNTPVRMLVVAGAKFKEALKPWLTWKAQKGFYLDVHYTDEAEVGTTNASIKAFIHKKYNDGLAASAAPVFLALVGDTDVISGEKGKKTKKVTDLYYSAVDGDYFPEMYTFRMSASSPEELTNIIDKVLMYEKATMPDKSYLEKVLLIAGADYSWNSQVGQPTIKYGMQYYYNQEHGYTDVYNYLKAPYTGCYSHLNTGVSFANYTAHGSETAWADPLLTTSQLKALTNKDKYFLAIGNCCITAQFDYVQPCFGEVITRVKEKGAYAYIGSSPNSYWGEDYYWSVGANAVFGVQPTFEGTSMGSYDATFLEDSYNTVNSIMWAGNLAATHAGNIGNITHIGAHYYWEAYHVLGDGSVMPYRAMPKTNTYTLPASLPQNQASYSIQASAGSYVAISKDGVLYGTGVANASGVATVSMTKQITENGNYDVVITRSNYLPVIKQIQVGEPHHHHHH

Source Source

Source organism organism	Porphyromonas gingivalis
NCBI taxonomy ID ncbi_taxonomy_id	837
Host organism host_organism	Porphyromonas gingivalis ATCC 33277

Entity 2 Entity 2 non-polymer

Description description	UNKNOWN ATOM OR ION
Molecular weight formula_weight	23.0 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	4

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	;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 ;
Molecular weight formula_weight	630.7 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	nat
Copy count entity_count	6

Entity 8 Entity 8 non-polymer

Description description	(2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
Molecular weight formula_weight	154.3 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	1580

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Unit-cell length a length_a	86.670 Å
Unit-cell length b length_b	87.050 Å
Unit-cell length c length_c	129.210 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.200 Å
Low-resolution limit resolution_low	72.190 Å
R factor r_factor	0.1460
R_work r_work	0.1460
R_free r_free	0.1480

Porphyromonas gingivalis gingipain K (Kgp) in complex with inhibitor KYT-36

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

Lys-gingipain W83

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

7. Citations (3)

Porphyromonas gingivalis gingipain K (Kgp) in complex with inhibitor KYT-36

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

Lys-gingipain W83

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

7. Citations (3)