SAXSdb — 1f8q

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

ALPHA-MOMORCHARIN

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	Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 24–286	Not recorded	;alpha-D-xylopyranose-(1-2)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 PTD PENTANEDIAL × 3 CCN ACETONITRILE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.1；295 K；PEG 3350, Tris-HCl, ATP, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K	Resolution 2.20 Å R-free 0.272

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 1F8Q	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AHA THE N-GLYCOSIDASE MECHANISM OF RIBOSOME-INACTIVATING PROTEINS IMPLIED BY CRYSTAL STRUCTURES OF ALPHA-MOMORCHARIN Deposited 1994-01-07	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 24–269（246 aa）	Not recorded	ADE ADENINE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å
1AHB THE N-GLYCOSIDASE MECHANISM OF RIBOSOME-INACTIVATING PROTEINS IMPLIED BY CRYSTAL STRUCTURES OF ALPHA-MOMORCHARIN Deposited 1994-01-07	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 24–269（246 aa）	Not recorded	FMP FORMYCIN-5'-MONOPHOSPHATE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å
1AHC THE N-GLYCOSIDASE MECHANISM OF RIBOSOME-INACTIVATING PROTEINS IMPLIED BY CRYSTAL STRUCTURES OF ALPHA-MOMORCHARIN Deposited 1994-01-07	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 24–269（246 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
1MOM CRYSTAL STRUCTURE OF MOMORDIN, A TYPE I RIBOSOME INACTIVATING PROTEIN FROM THE SEEDS OF MOMORDICA CHARANTIA Deposited 1994-03-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 24–269（246 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.16 Å
1MRG STUDIES ON CRYSTAL STRUCTURES ACTIVE CENTER GEOMETRY AND DEPURINE MECHANISM OF TWO RIBOSOME-INACTIVATING PROTEINS Deposited 1994-07-01	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 24–286（263 aa）	Not recorded	ADN ADENOSINE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å
1MRH STUDIES ON CRYSTAL STRUCTURES ACTIVE CENTER GEOMETRY AND DEPURINE MECHANISM OF TWO RIBOSOME-INACTIVATING PROTEINS Deposited 1994-07-01	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 24–286（263 aa）	Not recorded	FMC (1S)-1-(7-amino-1H-pyrazolo[4,3-d]pyrimidin-3-yl)-1,4-anhydro-D-ribitol × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
1MRI STUDIES ON CRYSTAL STRUCTURES ACTIVE CENTER GEOMETRY AND DEPURINE MECHANISM OF TWO RIBOSOME-INACTIVATING PROTEINS Deposited 1994-07-01	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 24–286（263 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å
4YP2 Cleavage of nicotinamide adenine dinucleotides by the ribosome inactivating protein from Momordica charantia Deposited 2015-03-12	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 B 24–269（246 aa） Fragment：UNP residues 24-269	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NCA NICOTINAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG 4000, sodium phosphate	Resolution 1.35 Å R-free 0.168
5CF9 Cleavage of nicotinamide adenine dinucleotide by the ribosome inactivating protein of Momordica charantia - enzyme-NADP+ co-crystallisation. Deposited 2015-07-08	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 B 24–269（246 aa） Fragment：residues 24-269	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NCA NICOTINAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；PEG 4000, sodium phosphate	Resolution 1.52 Å R-free 0.168
6LOQ crystal structure of alpha-momorcharin in complex with cAMP Deposited 2020-01-07	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 1–286（286 aa）	Not recorded	CMP ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.2 M Magnesium Acetate, 20% PEG 8000, 0.1 M Sodium cacodylate, pH 6.5	Resolution 1.33 Å R-free 0.257
6LOR crystal structure of alpha-momorcharin in complex with ADP Deposited 2020-01-07	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 1–286（286 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.2 M Magnesium Acetate, 20% PEG 8000, 0.1 M Sodium cacodylate,pH 6.5	Resolution 1.35 Å R-free 0.251
6LOV crystal structure of alpha-momorcharin in complex with xanthosine Deposited 2020-01-07	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 1–286（286 aa）	Not recorded	4UO 2,3-dihydroxanthosine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.2 M Magnesium Acetate, 20% PEG 8000, 0.1 M Sodium cacodylate, pH 6.5	Resolution 1.35 Å R-free 0.259
6LOW crystal structure of alpha-momorcharin in complex with GMP Deposited 2020-01-07	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 1–286（286 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 5GP GUANOSINE-5'-MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.2 M Magnesium Acetate, 20% PEG 8000, 0.1 M Sodium cacodylate, pH 6.5	Resolution 1.39 Å R-free 0.210
6LOY crystal structure of alpha-momorcharin in complex with dAMP Deposited 2020-01-07	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 1–286（286 aa）	Not recorded	D5M 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.2 M Magnesium Acetate, 20% PEG 8000, 0.1 M Sodium cacodylate, pH 6.5	Resolution 1.35 Å R-free 0.349
6LOZ crystal structure of alpha-momorcharin in complex with adenine Deposited 2020-01-07	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 1–286（286 aa）	Not recorded	ADE ADENINE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.2 M Magnesium Acetate, 20% PEG 8000, 0.1 M Sodium cacodylate, pH 6.5	Resolution 1.08 Å R-free 0.222
6LP0 crystal structure of alpha-momorcharin in complex with AMP Deposited 2020-01-07	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 1–286（286 aa）	Not recorded	AMP ADENOSINE MONOPHOSPHATE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.2 M Magnesium Acetate, 20% PEG 8000, 0.1 M Sodium cacodylate, pH 6.5	Resolution 1.52 Å R-free 0.299

16 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RIP1_MOMCH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–263； UniProt 24–286

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	1f8q
Deposition date deposition_date	2000-07-03
Structure title title	CRYSTAL STRUCTURE OF ALPHA-MOMORCHARIN IN ACETONITRILE-WATER MIXTURE
Keywords keywords	RIBOSOME-INACTIVATING PROTEIN, ORGANIC SLOVENT, MOMORCHARIN, 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	19.67 Å
Radius of gyration Rg (electron density) rg_electron	18.43 Å
Forward intensity I(0) i0	13678900.00
Molecular weight molecular_weight	28438.0 kDa
Excluded volume excluded_volume	35983 Å³
Envelope volume envelope_volume	41287 Å³
Hydration-shell volume shell_volume	18775 Å³
Envelope diameter envelope_diameter	70.6 Å
Shell Rg shell_rg	24.79 Å
Envelope Rg envelope_rg	18.86 Å
Shape Rg shape_rg	18.40 Å
Total Rg total_rg	19.51 Å
Total atoms total_atoms	2006
Residues n_residues	246
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	67.8 Å
Rg (real space) rg_real	19.60 Å
Rg uncertainty (real space) rg_real_error	0.45 Å
I(0) (real space) i0_real	1.3680e+07
I(0) uncertainty (real space) i0_real_error	1.6150e+05
Rg (reciprocal space) rg_reciprocal	19.62 Å
I(0) (reciprocal space) i0_reciprocal	13680000.0000
Solution quality estimate total_estimate	0.6162
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	24.9 Å
Skewness Skewness skewness	0.300
Kurtosis Kurtosis kurtosis	-0.147
Angular range angular_range	— – 0.4050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3492000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.730; Stabil: 1.000; Sysdev: 0.278; Positv: 1.000; Valcen: 0.982; Smooth: 0.000

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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	ALPHA-MOMORCHARIN
Molecular weight formula_weight	29118.0 kDa
EC 编号 ec_number	3.2.2.22
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	2102

DVSFRLSGADPRSYGMFIKDLRNALPFREKVYNIPLLLPSVSGAGRYLLMHLFNRDGKTITVAVDVTNVYIMGYLADTTSYFFNEPAAELASQYVFRDARRKITLPYSGDYERLQIAAGKPREKIPIGLPALDSAISTLLHYDSTAAAGALLVLIQTTAEAARFKYIEQQIQERAYRDEVPSLATISLENSWSGLSKQIQLAQGNNGIFRTPIVLVDNKGNRVQITNVTSKVVTSNIQLLLNTRNIAEGDNGDVSTTHGFSSY

Entity 2 Entity 2 branched

Description description	;alpha-D-xylopyranose-(1-2)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	718.7 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	PENTANEDIAL
Molecular weight formula_weight	100.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	ACETONITRILE
Molecular weight formula_weight	41.1 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	96

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1f8qa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.165 — Ribosome inactivating proteins (RIP)
Superfamily Superfamily superfamily	d.165.1 — Ribosome inactivating proteins (RIP)
Family Family family	d.165.1.1 — Plant cytotoxins

CATH v4.4 (2 domains)

Domain ID domain_id	1f8qA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	420 — Ricin (A subunit); domain 1
Homologous superfamily homologous superfamily	10 — Ricin (A subunit), domain 1

Domain ID domain_id	1f8qA02
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	470 — Ricin (A Subunit), domain 2
Homologous superfamily homologous superfamily	10 — Ricin (A Subunit), domain 2

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8. Citations (2)

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Unit-cell length a length_a	131.510 Å
Unit-cell length b length_b	131.510 Å
Unit-cell length c length_c	39.810 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	9

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.2040
R_work r_work	0.1980
R_free r_free	0.2720

fit	/app/data/saxs_computation/f8/1f8q/1f8q.fit
pddf	/app/data/pr_computation/f8/1f8q/1f8q.pr.out
profile	/app/data/saxs_computation/f8/1f8q/1f8q.dat

CRYSTAL STRUCTURE OF ALPHA-MOMORCHARIN IN ACETONITRILE-WATER MIXTURE