SAXSdb — 2nyq

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

Aminopeptidase

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 107–405	Fragment：Bacterial leucyl aminopeptidase, residues 97-405	Tetrapeptide × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8；296 K；5 d., 10/100/100 mM KSCN, 0.4/4.5/4.5 M NaCl, 10/100 mM Tris/100 mM Tricine, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 296K	Resolution 2.50 Å R-free 0.256

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 2NYQ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AMP CRYSTAL STRUCTURE OF AEROMONAS PROTEOLYTICA AMINOPEPTIDASE: A PROTOTYPICAL MEMBER OF THE CO-CATALYTIC ZINC ENZYME FAMILY Deposited 1994-04-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 107–397（291 aa）	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å
1CP6 1-BUTANEBORONIC ACID BINDING TO AEROMONAS PROTEOLYTICA AMINOPEPTIDASE Deposited 1999-06-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 107–397（291 aa）	Not recorded	ZN ZINC ION × 2 BUB 1-BUTANE BORONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；100 MM TRIS PH 8.0, 100 MM KSCN, 4.5 M NACL	Resolution 1.90 Å R-free 0.229
1FT7 AAP COMPLEXED WITH L-LEUCINEPHOSPHONIC ACID Deposited 2000-09-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 107–397（291 aa）	Not recorded	ZN ZINC ION × 2 K POTASSIUM ION × 1 PLU LEUCINE PHOSPHONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；KSCN, NaCl, Tris, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.232
1IGB AEROMONAS PROTEOLYTICA AMINOPEPTIDASE COMPLEXED WITH THE INHIBITOR PARA-IODO-D-PHENYLALANINE HYDROXAMATE Deposited 1996-02-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 107–397（291 aa）	Not recorded	ZN ZINC ION × 4 IPO PARA-IODO-D-PHENYLALANINE HYDROXAMIC ACID × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å R-free 0.241
1LOK The 1.20 Angstrom Resolution Crystal Structure of the Aminopeptidase from Aeromonas proteolytica Complexed with Tris: A Tale of Buffer Inhibition Deposited 2002-05-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 107–397（291 aa）	Not recorded	ZN ZINC ION × 2 NA SODIUM ION × 1 SCN THIOCYANATE ION × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；Tris, potassium thiocyanate, sodium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.20 Å R-free 0.198
1RTQ The 0.95 Angstrom Resolution Crystal Structure of the Aminopeptidase from Aeromonas proteolytica Deposited 2003-12-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 107–405（299 aa） Fragment：Aminopeptidase	Not recorded	SCN THIOCYANATE ION × 2 ZN ZINC ION × 2 NA SODIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；HEPES, Potassium Thiocyanate, Sodium Chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 0.95 Å R-free 0.151
1TXR X-ray crystal structure of bestatin bound to AAP Deposited 2004-07-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 107–405（299 aa）	Not recorded	ZN ZINC ION × 2 BES 2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL-PENTANOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；tris, KSCN, NaCl, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.245
1XRY Crystal structure of Aeromonas proteolytica aminopeptidase in complex with bestatin Deposited 2004-10-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 107–405（299 aa）	Not recorded	ZN ZINC ION × 2 BES 2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL-PENTANOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；NaCl, KSCN, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å R-free 0.197
2ANP Functional Glutamate 151 to Histidine mutant of the aminopeptidase from Aeromonas Proteolytica. Deposited 2005-08-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 107–397（291 aa）	Mutation：E151H	ZN ZINC ION × 2 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；4.5 M NaCL, 100 mM KSCN, 100 mM HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 25K	Resolution 1.90 Å R-free 0.205
2DEA Crystal Structure of the Aminopeptidase of Aeromonas proteolytica at pH 4.7 Deposited 2006-02-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 107–405（299 aa）	Not recorded	ZN ZINC ION × 2 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.7；298 K；NaAcetate, KSCN, NaCl, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.24 Å R-free 0.163
2IQ6 Crystal Structure of the Aminopeptidase from Vibrio proteolyticus in Complexation with Leucyl-leucyl-leucine. Deposited 2006-10-13	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 107–397（291 aa）	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；KSCN, NACL, TRIS, PH 8.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K, TRIS REPLACED BY HEPES	Resolution 2.00 Å R-free 0.247
2PRQ X-ray crystallographic characterization of the Co(II)-substituted Tris-bound form of the aminopeptidase from Aeromonas proteolytica Deposited 2007-05-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 107–397（291 aa） Fragment：residues 107-397	Not recorded	CO COBALT (II) ION × 2 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；100 mM Tris pH 8.0, 100 mM KSCN, 4.5 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298KK	Resolution 2.15 Å R-free 0.273
3B35 Crystal structure of the M180A mutant of the aminopeptidase from Vibrio proteolyticus Deposited 2007-10-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 107–397（291 aa） Fragment：Residues 107-397	Mutation：M286A	ZN ZINC ION × 2 NA SODIUM ION × 7 SCN THIOCYANATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；HEPES, KSCN, NaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.10 Å R-free 0.166
3B3C Crystal structure of the M180A mutant of the aminopeptidase from Vibrio proteolyticus in complex with leucine phosphonic acid Deposited 2007-10-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 107–397（291 aa） Fragment：Residues 107-397	Mutation：M286A	ZN ZINC ION × 2 K POTASSIUM ION × 1 SCN THIOCYANATE ION × 1 NA SODIUM ION × 6 PLU LEUCINE PHOSPHONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；HEPES, KSCN, NaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.46 Å R-free 0.226
3B3S Crystal structure of the M180A mutant of the aminopeptidase from Vibrio proteolyticus in complex with leucine Deposited 2007-10-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 107–397（291 aa） Fragment：Residues 107-397	Mutation：M286A	ZN ZINC ION × 2 NA SODIUM ION × 8 SCN THIOCYANATE ION × 2 LEU LEUCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；HEPES, KSCN, NaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.18 Å R-free 0.196
3B3T Crystal structure of the D118N mutant of the aminopeptidase from Vibrio proteolyticus Deposited 2007-10-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 107–397（291 aa） Fragment：Residues 107-397	Mutation：D224N	ZN ZINC ION × 2 NA SODIUM ION × 3 SCN THIOCYANATE ION × 2 ILE ISOLEUCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；HEPES, KSCN, NaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.17 Å R-free 0.161
3B3V Crystal structure of the S228A mutant of the aminopeptidase from Vibrio proteolyticus Deposited 2007-10-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 107–397（291 aa） Fragment：Residues 107-397	Mutation：S334A	ZN ZINC ION × 2 NA SODIUM ION × 3 SCN THIOCYANATE ION × 2 VAL VALINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；HEPES, KSCN, NaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.22 Å R-free 0.171
3B3W Crystal structure of the S228A mutant of the aminopeptidase from Vibrio proteolyticus in complex with leucine Deposited 2007-10-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 107–397（291 aa） Fragment：Residues 107-397	Mutation：S334A	ZN ZINC ION × 2 SCN THIOCYANATE ION × 1 NA SODIUM ION × 2 LEU LEUCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；HEPES, KSCN, NaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.75 Å R-free 0.234
3B7I Crystal structure of the S228A mutant of the aminopeptidase from Vibrio proteolyticus in complex with leucine phosphonic acid Deposited 2007-10-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 107–397（291 aa） Fragment：Residues 107-397	Mutation：S228A	ZN ZINC ION × 2 K POTASSIUM ION × 1 NA SODIUM ION × 2 SCN THIOCYANATE ION × 1 PLU LEUCINE PHOSPHONIC ACID × 1 LEU LEUCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；HEPES, NaCl, KSCN, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.75 Å R-free 0.209
3FH4 Crystal Structure of Recombinant Vibrio proteolyticus aminopeptidase Deposited 2008-12-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 107–405（299 aa）	Not recorded	ZN ZINC ION × 2 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；VpAP (0.5 mM) in 10 mM Tris buffer, pH 8.0, containing 10 mM KSCN and 400 mM NaCl was equilibrated with 100 mM Tris buffer, pH 8.0, containing 100 mM KSCN and 4.5 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.95 Å R-free 0.228
3VH9 Crystal structure of Aeromonas proteolytica aminopeptidase complexed with 8-quinolinol Deposited 2011-08-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 107–405（299 aa） Fragment：UNP RESIDUES 107-405	Not recorded	ZN ZINC ION × 2 HQY quinolin-8-ol × 1 NA SODIUM ION × 9 CL CHLORIDE ION × 9 SCN THIOCYANATE ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；100mM Tris-HCl, 100mM KSCN, 4.5M NaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.29 Å R-free 0.153

21 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	AMPX_VIBPR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–299； UniProt 107–405

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	2nyq
Deposition date deposition_date	2006-11-21
Structure title title	Structure of Vibrio proteolyticus aminopeptidase with a bound Trp fragment of dLWCF
Keywords keywords	Trp, VpAP, non-covalent, HYDROLASE; HYDROLASE
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	18.34 Å
Radius of gyration Rg (electron density) rg_electron	17.17 Å
Forward intensity I(0) i0	18664400.00
Molecular weight molecular_weight	31690.0 kDa
Excluded volume excluded_volume	38979 Å³
Envelope volume envelope_volume	41681 Å³
Hydration-shell volume shell_volume	19634 Å³
Envelope diameter envelope_diameter	58.8 Å
Shell Rg shell_rg	24.12 Å
Envelope Rg envelope_rg	17.40 Å
Shape Rg shape_rg	17.17 Å
Total Rg total_rg	18.05 Å
Total atoms total_atoms	2226
Residues n_residues	292
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	56.9 Å
Rg (real space) rg_real	18.20 Å
Rg uncertainty (real space) rg_real_error	0.27 Å
I(0) (real space) i0_real	1.8660e+07
I(0) uncertainty (real space) i0_real_error	2.1710e+05
Rg (reciprocal space) rg_reciprocal	18.22 Å
I(0) (reciprocal space) i0_reciprocal	18660000.0000
Solution quality estimate total_estimate	0.8943
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	55.3 Å
Skewness Skewness skewness	0.075
Kurtosis Kurtosis kurtosis	-0.450
Angular range angular_range	— – 0.4350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5231000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.883; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.996

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Aminopeptidase
Molecular weight formula_weight	32238.2 kDa
EC 编号 ec_number	3.4.11.10
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2378

MPPITQQATVTAWLPQVDASQITGTISSLESFTNRFYTTTSGAQASDWIASEWQALSASLPNASVKQVSHSGYNQKSVVMTITGSEAPDEWIVIGGHLDSTIGSHTNEQSVAPGADDDASGIAAVTEVIRVLSENNFQPKRSIAFMAYAAEEVGLRGSQDLANQYKSEGKNVVSALQLDMTNYKGSAQDVVFITDYTDSNFTQYLTQLMDEYLPSLTYGFDTCGYACSDHASWHNAGYPAAMPFESKFNDYNPRIHTTQDTLANSDPTGSHAKKFTQLGLAYAIEMGSATGDTPTPGNQ

Entity 2 Entity 2 polymer

Description description	Tetrapeptide
Molecular weight formula_weight	567.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

LWCF

Entity 3 Entity 3 non-polymer

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

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	152

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2nyqa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.56 — Phosphorylase/hydrolase-like
Superfamily Superfamily superfamily	c.56.5 — Zn-dependent exopeptidases
Family Family family	c.56.5.4 — Bacterial dinuclear zinc exopeptidases

CATH v4.4 (1 domains)

Domain ID domain_id	2nyqA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	10 — Zn peptidases

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8. Citations (1)

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Unit-cell length a length_a	107.800 Å
Unit-cell length b length_b	107.800 Å
Unit-cell length c length_c	99.600 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 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1910
R_work r_work	0.1910
R_free r_free	0.2560

fit	/app/data/saxs_computation/ny/2nyq/2nyq.fit
pddf	/app/data/pr_computation/ny/2nyq/2nyq.pr.out
profile	/app/data/saxs_computation/ny/2nyq/2nyq.dat

Structure of Vibrio proteolyticus aminopeptidase with a bound Trp fragment of dLWCF

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

Aminopeptidase

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)