SAXSdb — 1f2p

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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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–284	Not recorded	ZN ZINC ION × 2 CA CALCIUM ION × 1 PHE PHENYLALANINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；PEG4000, Sodium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.225

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 1F2P	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CP7 AMINOPEPTIDASE FROM STREPTOMYCES GRISEUS Deposited 1999-06-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–284（284 aa）	Not recorded	ZN ZINC ION × 2 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；16% PEG 4K, 0.1 M SODIUM ACETATE PH 5.5	Resolution 1.58 Å R-free 0.171
1F2O CRYSTAL STRUCTURE OF THE STREPTOMYCES GRISEUS AMINOPEPTIDASE COMPLEXED WITH L-LEUCINE Deposited 2000-05-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–284（284 aa）	Not recorded	ZN ZINC ION × 2 CA CALCIUM ION × 1 LEU LEUCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；PEG4000, Ammunium Sulfate , VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.70 Å R-free 0.175
1QQ9 STREPTOMYCES GRISEUS AMINOPEPTIDASE COMPLEXED WITH METHIONINE Deposited 1999-06-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–284（284 aa）	Not recorded	ZN ZINC ION × 2 CA CALCIUM ION × 1 MET METHIONINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；PEG 4000, AMMONIUM SULFATE, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.53 Å R-free 0.173
1TF8 Streptomyces griseus aminopeptidase complexed with L-tryptophan Deposited 2004-05-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–284（284 aa）	Not recorded	ZN ZINC ION × 2 CA CALCIUM ION × 1 TRP TRYPTOPHAN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；PEG 4000, sodium acetate, pH 5.5, vapor diffusion, hanging drop, temperature 298K	Resolution 1.30 Å R-free 0.174
1TF9 Streptomyces griseus aminopeptidase complexed with P-Iodo-L-Phenylalanine Deposited 2004-05-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–284（284 aa）	Not recorded	ZN ZINC ION × 2 CA CALCIUM ION × 1 PHI IODO-PHENYLALANINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；PEG 4000, sodium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.30 Å R-free 0.172
1TKF Streptomyces griseus aminopeptidase complexed with D-tryptophan Deposited 2004-06-08	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–284（284 aa）	Not recorded	ZN ZINC ION × 2 CA CALCIUM ION × 1 DTR D-TRYPTOPHAN × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；PEG 4000, sodium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.20 Å R-free 0.168
1TKH Streptomyces griseus aminopeptidase complexed with D-Phenylalanine Deposited 2004-06-08	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–284（284 aa）	Not recorded	ZN ZINC ION × 2 CA CALCIUM ION × 1 DPN D-PHENYLALANINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；PEG 4000, sodium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.25 Å R-free 0.156
1TKJ Streptomyces griseus aminopeptidase complexed with D-Methionine Deposited 2004-06-08	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–284（284 aa）	Not recorded	ZN ZINC ION × 2 CA CALCIUM ION × 1 MED D-METHIONINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；PEG 4000, sodium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.15 Å R-free 0.151
1XBU Streptomyces griseus aminopeptidase complexed with p-iodo-D-phenylalanine Deposited 2004-08-31	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–277（277 aa）	Not recorded	ZN ZINC ION × 2 CA CALCIUM ION × 1 IOY P-IODO-D-PHENYLALANINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；PEG 4000, sodium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.20 Å R-free 0.167
1XJO STRUCTURE OF AMINOPEPTIDASE Deposited 1996-10-09	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–284（284 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 2 PO4 PHOSPHATE ION × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；16% PEG 4K, 0.1 M SODIUM ACETATE, pH 5.5	Resolution 1.75 Å

10 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	APX_STRGR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–284； UniProt 1–284

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	1f2p
Deposition date deposition_date	2000-05-28
Structure title title	CRYSTAL STRUCTURE OF THE STREPTOMYCES GRISEUS AMINOPEPTIDASE COMPLEXED WITH L-PHENYLALANINE
Keywords keywords	HYDROLASE, AMINOPEPTIDASE, DOUBLE-ZINC METALLOPROTEINASE; 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	18.37 Å
Radius of gyration Rg (electron density) rg_electron	17.20 Å
Forward intensity I(0) i0	15776700.00
Molecular weight molecular_weight	29082.0 kDa
Excluded volume excluded_volume	35918 Å³
Envelope volume envelope_volume	39905 Å³
Hydration-shell volume shell_volume	18970 Å³
Envelope diameter envelope_diameter	56.2 Å
Shell Rg shell_rg	23.88 Å
Envelope Rg envelope_rg	17.46 Å
Shape Rg shape_rg	17.18 Å
Total Rg total_rg	18.20 Å
Total atoms total_atoms	2048
Residues n_residues	274
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	56.3 Å
Rg (real space) rg_real	18.25 Å
Rg uncertainty (real space) rg_real_error	0.27 Å
I(0) (real space) i0_real	1.5780e+07
I(0) uncertainty (real space) i0_real_error	1.8230e+05
Rg (reciprocal space) rg_reciprocal	18.26 Å
I(0) (reciprocal space) i0_reciprocal	15780000.0000
Solution quality estimate total_estimate	0.9029
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	54.8 Å
Skewness Skewness skewness	0.120
Kurtosis Kurtosis kurtosis	-0.459
Angular range angular_range	— – 0.4350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4234000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.917; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.998

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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	AMINOPEPTIDASE
Molecular weight formula_weight	29750.7 kDa
EC 编号 ec_number	3.4.11.-
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	2343

APDIPLANVKAHLTQLSTIAANNGGNRAHGRPGYKASVDYVKAKLDAAGYTTTLQQFTSGGATGYNLIANWPGGDPNKVLMAGAHLDSVSSGAGINDNGSGSAAVLETALAVSRAGYQPDKHLRFAWWGAEELGLIGSKFYVNNLPSADRSKLAGYLNFDMIGSPNPGYFVYDDDPVIEKTFKNYFAGLNVPTEIETEGDGRSDHAPFKNVGVPVGGLFTGAGYTKSAAQAQKWGGTAGQAFDRCYHSSCDSLSNINDTALDRNSDAAAHAIWTLSSGTGEPPT

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
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	1

Entity 4 Entity 4 non-polymer

Description description	PHENYLALANINE
Molecular weight formula_weight	165.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	295

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1f2pa_
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	1f2pA00
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 (4)

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Unit-cell length a length_a	62.180 Å
Unit-cell length b length_b	62.180 Å
Unit-cell length c length_c	146.980 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	48.000 Å
R factor r_factor	0.1870
R_work r_work	0.1870
R_free r_free	0.2250

fit	/app/data/saxs_computation/f2/1f2p/1f2p.fit
pddf	/app/data/pr_computation/f2/1f2p/1f2p.pr.out
profile	/app/data/saxs_computation/f2/1f2p/1f2p.dat

CRYSTAL STRUCTURE OF THE STREPTOMYCES GRISEUS AMINOPEPTIDASE COMPLEXED WITH L-PHENYLALANINE

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