SAXSdb — 4yp2

▼

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

Ribosome-inactivating protein momordin I

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 B； UniProt 24–269	Fragment：UNP residues 24-269	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

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 4YP2	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 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 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 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
1F8Q CRYSTAL STRUCTURE OF ALPHA-MOMORCHARIN IN ACETONITRILE-WATER MIXTURE Deposited 2000-07-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 24–286（263 aa）	Not recorded	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
1MOM CRYSTAL STRUCTURE OF MOMORDIN, A TYPE I RIBOSOME INACTIVATING PROTEIN FROM THE SEEDS OF MOMORDICA CHARANTIA Deposited 1994-03-04	Different construct Different oligomeric state 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 construct 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 construct 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 construct 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
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 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 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 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 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 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 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 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 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 B； PDBConstruct 1–246； UniProt 24–269

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	4yp2
Deposition date deposition_date	2015-03-12
Structure title title	Cleavage of nicotinamide adenine dinucleotides by the ribosome inactivating protein from Momordica charantia
Keywords keywords	Ribosome inactivating protein, N-glycosidase, nicotinamide, complex, hydrolase; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	19.11 Å
Radius of gyration Rg (electron density) rg_electron	17.78 Å
Forward intensity I(0) i0	12953500.00
Molecular weight molecular_weight	27700.0 kDa
Excluded volume excluded_volume	35033 Å³
Envelope volume envelope_volume	39570 Å³
Hydration-shell volume shell_volume	18448 Å³
Envelope diameter envelope_diameter	65.3 Å
Shell Rg shell_rg	24.15 Å
Envelope Rg envelope_rg	18.14 Å
Shape Rg shape_rg	17.76 Å
Total Rg total_rg	18.82 Å
Total atoms total_atoms	3939
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

▼

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

Maximum dimension Dmax dmax	62.6 Å
Rg (real space) rg_real	19.01 Å
Rg uncertainty (real space) rg_real_error	0.42 Å
I(0) (real space) i0_real	1.2950e+07
I(0) uncertainty (real space) i0_real_error	1.6380e+05
Rg (reciprocal space) rg_reciprocal	19.03 Å
I(0) (reciprocal space) i0_reciprocal	12950000.0000
Solution quality estimate total_estimate	0.8017
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	24.3 Å
Skewness Skewness skewness	0.228
Kurtosis Kurtosis kurtosis	-0.271
Angular range angular_range	— – 0.4150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3443000.0000
Real-space data points n_real_points	73
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.806; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Ribosome-inactivating protein momordin I
Molecular weight formula_weight	27396.3 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	B
Atom count atom_count	4286

DVSFRLSGADPRSYGMFIKDLRNALPFREKVYNIPLLLPSVSGAGRYLLMHLFNYDGKTITVAVDVTNVYIMGYLADTTSYFFNEPAAELASQYVFRDARRKITLPYSGNYERLQIAAGKPREKIPIGLPALDSAISTLLHYDSTAAAGALLVLIQTTAEAARFKYIEQQIQERAYRDEVPSLATISLENSWSGLSKQIQLAQGNNGIFRTPIVLVDNKGNRVQITNVTSKVVTSNIQLLLNTRNI

Entity 2 Entity 2 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	NICOTINAMIDE
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	271

▼

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d4yp2b_
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	4yp2B01
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	4yp2B02
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

▶

8. Citations (1)

▶

Unit-cell length a length_a	130.100 Å
Unit-cell length b length_b	130.100 Å
Unit-cell length c length_c	37.570 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	1.350 Å
Low-resolution limit resolution_low	37.557 Å
R factor r_factor	0.1417
R_work r_work	0.1403
R_free r_free	0.1682

fit	/app/data/saxs_computation/yp/4yp2/4yp2.fit
pddf	/app/data/pr_computation/yp/4yp2/4yp2.pr.out
profile	/app/data/saxs_computation/yp/4yp2/4yp2.dat

Cleavage of nicotinamide adenine dinucleotides by the ribosome inactivating protein from Momordica charantia

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

Ribosome-inactivating protein momordin I

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