7p4o

Crystal structure of Autotaxin and 9(R)-delta6a,10a-THC

Method: X-RAY DIFFRACTION

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

Ectonucleotide pyrophosphatase/phosphodiesterase family member 2

Rattus norvegicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Monomer	Protein 1 其他Polymer 1	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 7alpha-hydroxycholesterol × 1 ZINC ION × 2 (9~{R},10~{a}~{S})-6,6,9-trimethyl-3-pentyl-6~{a},7,8,9,10,10~{a}-hexahydrobenzo[c]chromen-1-ol × 1 THIOCYANATE ION × 2 CALCIUM ION × 1 GLYCEROL × 2 IODIDE ION × 12 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ENPP2_RAT
Isoform	Q64610-2
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–827； UniProt 36–862

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	7p4o
Deposition date deposition_date	2021-07-12
Structure title title	Crystal structure of Autotaxin and 9(R)-delta6a,10a-THC
Keywords keywords	9(R)-delta6a, 10a-THC, inhibitor, 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.

7p4o__assembly_1__model_1

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

Download this curve (.dat)

7p4o__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7p4o__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.55 Å
Rg (electron density)	29.56 Å
Total Rg	30.38 Å
Atom count	6617
Residues	776
Excluded volume	113140 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7p4o__assembly_1__model_1`	monomeric （1）	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 (10)

Entity 1 Entity 1 polymer

Description description	Ectonucleotide pyrophosphatase/phosphodiesterase family member 2
Molecular weight formula_weight	95037.7 kDa
EC 编号 ec_number	3.1.4.39
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	7078

AEWDEGPPTVLSDSPWTNTSGSCKGRCFELQEVGPPDCRCDNLCKSYSSCCHDFDELCLKTARGWECTKDRCGEVRNEENACHCSEDCLSRGDCCTNYQVVCKGESHWVDDDCEEIKVPECPAGFVRPPLIIFSVDGFRASYMKKGSKVMPNIEKLRSCGTHAPYMRPVYPTKTFPNLYTLATGLYPESHGIVGNSMYDPVFDASFHLRGREKFNHRWWGGQPLWITATKQGVRAGTFFWSVSIPHERRILTILQWLSLPDNERPSVYAFYSEQPDFSGHKYGPFGPEMTNPLREIDKTVGQLMDGLKQLRLHRCVNVIFVGDHGMEDVTCDRTEFLSNYLTNVDDITLVPGTLGRIRAKSINNSKYDPKTIIAALTCKKPDQHFKPYMKQHLPKRLHYANNRRIEDIHLLVDRRWHVARKPLDVYKKPSGKCFFQGDHGFDNKVNSMQTVFVGYGPTFKYRTKVPPFENIELYNVMCDLLGLKPAPNNGTHGSLNHLLRTNTFRPTMPDEVSRPNYPGIMYLQSEFDLGCTCDDKVEPKNKLEEFNKRLHTKGSTKERHLLYGRPAVLYRTSYDILYHTDFESGYSEIFLMPLWTSYTISKQAEVSSIPEHLTNCVRPDVRVSPGFSQNCLAYKNDKQMSYGFLFPPYLSSSPEAKYDAFLVTNMVPMYPAFKRVWAYFQRVLVKKYASERNGVNVISGPIFDYNYDGLRDTEDEIKQYVEGSSIPVPTHYYSIITSCLDFTQPADKCDGPLSVSSFILPHRPDNDESCASSEDESKWVEELMKMHTARVRDIEHLTGLDFYRKTSRSYSEILTLKTYLHTYESEI

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	Norway rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	7alpha-hydroxycholesterol
Molecular weight formula_weight	402.7 kDa
Source method src_method	nat
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	(9~{R},10~{a}~{S})-6,6,9-trimethyl-3-pentyl-6~{a},7,8,9,10,10~{a}-hexahydrobenzo[c]chromen-1-ol
Molecular weight formula_weight	316.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	THIOCYANATE ION
Molecular weight formula_weight	58.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 9 Entity 9 non-polymer

Description description	IODIDE ION
Molecular weight formula_weight	126.9 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 10 Entity 10 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	461

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	7p4oA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	570 — Extracellular Endonuclease; Chain A
Homologous superfamily homologous superfamily	10 — Extracellular Endonuclease, subunit A

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Unit-cell length a length_a	53.841 Å
Unit-cell length b length_b	62.361 Å
Unit-cell length c length_c	64.356 Å
Unit-cell angle α angle_alpha	103.70 °
Unit-cell angle β angle_beta	98.37 °
Unit-cell angle γ angle_gamma	93.44 °
Molecules per unit cell Z z_pdb	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	triclinic

Resolution resolution	1.690 Å
Low-resolution limit resolution_low	60.290 Å
R factor r_factor	0.1719
R_work r_work	0.1711
R_free r_free	0.2058

Crystal structure of Autotaxin and 9(R)-delta6a,10a-THC

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

Ectonucleotide pyrophosphatase/phosphodiesterase family member 2

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

7p4o__assembly_1__model_1

7p4o__assembly_1__model_1 | I(q)

7p4o__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

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 non-polymer

Entity 10 Entity 10 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (2)

Crystal structure of Autotaxin and 9(R)-delta6a,10a-THC

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

Ectonucleotide pyrophosphatase/phosphodiesterase family member 2

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

7p4o__assembly_1__model_1

7p4o__assembly_1__model_1 | I(q)

7p4o__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

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 non-polymer

Entity 10 Entity 10 water

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (2)