SAXSdb — 2d5l

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

dipeptidyl aminopeptidase IV, putative

Porphyromonas gingivalis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q7MUW6_PORGI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–706； UniProt 39–732

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	2d5l
Deposition date deposition_date	2005-11-02
Structure title title	Crystal Structure of Prolyl Tripeptidyl Aminopeptidase from Porphyromonas gingivalis
Keywords keywords	peptidase family S9, serine peptidase, prolyl oligopeptidase family, 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.

2d5l__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2d5l__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2d5l__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	38.53 Å
Rg (electron density)	38.15 Å
Total Rg	38.65 Å
Atom count	10570
Residues	1330
Excluded volume	187250 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2d5l__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	dipeptidyl aminopeptidase IV, putative
Molecular weight formula_weight	79604.8 kDa
EC 编号 ec_number	3.4.14.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	5704

MRGSHHHHHHGSLMPGGKEFYNFYPEYVVGLQWMGDNYVFIEGDDLVFNKANGKSAQTTRFSAADLNALMPEGCKFQTTDAFPSFRTLDAGRGLVVLFTQGGLVGFDMLARKVTYLFDTNEETASLDFSPVGDRVAYVRNHNLYIARGGKLGEGMSRAIAVTIDGTETLVYGQAVHQREFGIEKGTFWSPKGSCLAFYRMDQSMVKPTPIVDYHPLEAESKPLYYPMAGTPSHHVTVGIYHLATGKTVYLQTGEPKEKFLTNLSWSPDENILYVAEVNRAQNECKVNAYDAETGRFVRTLFVETDKHYVEPLHPLTFLPGSNNQFIWQSRRDGWNHLYLYDTTGRLIRQVTKGEWEVTNFAGFDPKGTRLYFESTEASPLERHFYCIDIKGGKTKDLTPESGMHRTQLSPDGSAIIDIFQSPTVPRKVTVTNIGKGSHTLLEAKNPDTGYAMPEIRTGTIMAADGQTPLYYKLTMPLHFDPAKKYPVIVYVYGGPHAQLVTKTWRSSVGGWDIYMAQKGYAVFTVDSRGSANRGAAFEQVIHRRLGQTEMADQMCGVDFLKSQSWVDADRIGVHGWSYGGFMTTNLMLTHGDVFKVGVAGGPVIDWNRYEIMYGERYFDAPQENPEGYDAANLLKRAGDLKGRLMLIHGAIDPVVVWQHSLLFLDACVKARTYPDYYVYPSHEHNVMGPDRVHLYETITRYFTDHL

Source Source

Source organism organism	Porphyromonas gingivalis
NCBI taxonomy ID ncbi_taxonomy_id	242619
Host organism host_organism	Escherichia coli

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	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	419

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2d5lA01
Class class	2 — Mainly Beta
Architecture architecture	140 — 8 Propeller
Topology topology	10 — Methanol Dehydrogenase; Chain A
Homologous superfamily homologous superfamily	30 — Dipeptidylpeptidase IV, N-terminal domain

Domain ID domain_id	2d5lA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

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Unit-cell length a length_a	149.394 Å
Unit-cell length b length_b	149.394 Å
Unit-cell length c length_c	159.684 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 63 2 2
Space-group number int_tables_number	182
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2030
R_free r_free	0.2280

Crystal Structure of Prolyl Tripeptidyl Aminopeptidase from Porphyromonas gingivalis

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

dipeptidyl aminopeptidase IV, putative

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

2d5l__assembly_1__model_1

2d5l__assembly_1__model_1 | I(q)

2d5l__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal Structure of Prolyl Tripeptidyl Aminopeptidase from Porphyromonas gingivalis

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

dipeptidyl aminopeptidase IV, putative

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

2d5l__assembly_1__model_1

2d5l__assembly_1__model_1 | I(q)

2d5l__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)