SAXSdb — 1atl

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

Snake venom metalloproteinase atrolysin-D

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	ZINC ION × 1 CALCIUM ION × 1 O-methyl-N-[(2S)-4-methyl-2-(sulfanylmethyl)pentanoyl]-L-tyrosine × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ZINC ION × 1 CALCIUM ION × 1 O-methyl-N-[(2S)-4-methyl-2-(sulfanylmethyl)pentanoyl]-L-tyrosine × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VM1AD_CROAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–202； UniProt 192–393 Author chain B； PDBConstruct 1–202； UniProt 192–393

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	1atl
Deposition date deposition_date	1995-05-26
Structure title title	Structural interaction of natural and synthetic inhibitors with the VENOM METALLOPROTEINASE, ATROLYSIN C (FORM-D)
Keywords keywords	METALLOENDOPEPTIDASE, HYDROLASE-HYDROLASE INHIBITOR complex; HYDROLASE/HYDROLASE INHIBITOR
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.

1atl__assembly_1__model_1

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

Download this curve (.dat)

1atl__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1atl__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	17.36 Å
Rg (electron density)	16.07 Å
Total Rg	17.08 Å
Atom count	1630
Residues	200
Excluded volume	28836 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1atl__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1atl__assembly_2__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 (5)

Entity 1 Entity 1 polymer

Description description	Snake venom metalloproteinase atrolysin-D
Molecular weight formula_weight	23147.3 kDa
EC 编号 ec_number	3.4.24.42
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3419

QNLPQRYIELVVVADHRVFMKYNSDLNTIRTRVHEIVNFINGFYRSLNIHVSLTDLEIWSNEDQINIQSASSDTLNAFAEWRETDLLNRKSHDNAQLLTAIELDEETLGLAPLGTMCDPKLSIGIVQDHSPINLLMGVTMAHELGHNLGMEHDGKDCLRGASLCIMRPGLTKGRSYEFSDDSMHYYERFLKQYKPQCILNKP

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
EC 编号 ec_number	3.4.24.42
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	O-methyl-N-[(2S)-4-methyl-2-(sulfanylmethyl)pentanoyl]-L-tyrosine
Molecular weight formula_weight	339.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	159

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1atla_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.92 — Zincin-like
Superfamily Superfamily superfamily	d.92.1 — Metalloproteases ('zincins'), catalytic domain
Family Family family	d.92.1.9 — Reprolysin-like

Domain ID domain_id	d1atlb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.92 — Zincin-like
Superfamily Superfamily superfamily	d.92.1 — Metalloproteases ('zincins'), catalytic domain
Family Family family	d.92.1.9 — Reprolysin-like

CATH v4.4 (2 domains)

Domain ID domain_id	1atlA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

Domain ID domain_id	1atlB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily	10 — Collagenase (Catalytic Domain)

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Unit-cell length a length_a	97.320 Å
Unit-cell length b length_b	97.320 Å
Unit-cell length c length_c	87.760 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 65
Space-group number int_tables_number	170
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1600
R_work r_work	0.1600
R_free r_free	—

Structural interaction of natural and synthetic inhibitors with the VENOM METALLOPROTEINASE, ATROLYSIN C (FORM-D)

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

Snake venom metalloproteinase atrolysin-D

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

1atl__assembly_1__model_1

1atl__assembly_1__model_1 | I(q)

1atl__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (2)

Structural interaction of natural and synthetic inhibitors with the VENOM METALLOPROTEINASE, ATROLYSIN C (FORM-D)

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

Snake venom metalloproteinase atrolysin-D

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

1atl__assembly_1__model_1

1atl__assembly_1__model_1 | I(q)

1atl__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (2)