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	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 A； UniProt 192–393	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 1 0QI O-methyl-N-[(2S)-4-methyl-2-(sulfanylmethyl)pentanoyl]-L-tyrosine × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.80 Å
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 192–393	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 1 0QI O-methyl-N-[(2S)-4-methyl-2-(sulfanylmethyl)pentanoyl]-L-tyrosine × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.80 Å

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 1ATL	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DTH METALLOPROTEASE Deposited 1996-02-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 191–393（203 aa） Chain B 191–393（203 aa）	Not recorded	ZN ZINC ION × 2 CA CALCIUM ION × 2 BAT 4-(N-HYDROXYAMINO)-2R-ISOBUTYL-2S-(2-THIENYLTHIOMETHYL)SUCCINYL-L-PHENYLALANINE-N-METHYLAMIDE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
1HTD STRUCTURAL INTERACTION OF NATURAL AND SYNTHETIC INHIBITORS WITH THE VENOM METALLOPROTEINASE, ATROLYSIN C (HT-D) Deposited 1994-01-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 192–393（202 aa） Chain B 192–393（202 aa）	Not recorded	ZN ZINC ION × 2 CA CALCIUM ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

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

Radius of gyration Rg (Guinier) rg_guinier	25.21 Å
Radius of gyration Rg (electron density) rg_electron	24.71 Å
Forward intensity I(0) i0	70786200.00
Molecular weight molecular_weight	43398.0 kDa
Excluded volume excluded_volume	41591 Å³
Envelope volume envelope_volume	68350 Å³
Hydration-shell volume shell_volume	24128 Å³
Envelope diameter envelope_diameter	85.0 Å
Shell Rg shell_rg	31.02 Å
Envelope Rg envelope_rg	24.74 Å
Shape Rg shape_rg	24.71 Å
Total Rg total_rg	25.24 Å
Total atoms total_atoms	3260
Residues n_residues	400
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	82.5 Å
Rg (real space) rg_real	25.34 Å
Rg uncertainty (real space) rg_real_error	0.76 Å
I(0) (real space) i0_real	7.0790e+07
I(0) uncertainty (real space) i0_real_error	1.1100e+06
Rg (reciprocal space) rg_reciprocal	25.30 Å
I(0) (reciprocal space) i0_reciprocal	70780000.0000
Solution quality estimate total_estimate	0.8663
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.9 Å
Skewness Skewness skewness	0.495
Kurtosis Kurtosis kurtosis	-0.343
Angular range angular_range	— – 0.3150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	11090000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.822; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.859; Smooth: 0.936

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. 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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7. 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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8. Citations (2)

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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	—

fit	/app/data/saxs_computation/at/1atl/1atl.fit
pddf	/app/data/pr_computation/at/1atl/1atl.pr.out
profile	/app/data/saxs_computation/at/1atl/1atl.dat

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