SAXSdb — 2bex

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

RIBONUCLEASE INHIBITOR

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	NONSECRETORY RIBONUCLEASE × 1 （P10153） GLYCEROL × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	NONSECRETORY RIBONUCLEASE × 1 （P10153） ALPHA-KETOMALONIC ACID × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RINI_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–460； UniProt 1–460 Author chain B； PDBConstruct 1–460； UniProt 1–460

NONSECRETORY RIBONUCLEASE

HOMO SAPIENS

UniProt P10153

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	RIBONUCLEASE INHIBITOR × 1 （P13489） GLYCEROL × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	RIBONUCLEASE INHIBITOR × 1 （P13489） ALPHA-KETOMALONIC ACID × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RNKD_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 2–135； UniProt 28–161 Author chain D； PDBConstruct 2–135； UniProt 28–161

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	2bex
Deposition date deposition_date	2004-12-01
Structure title title	Crystal structure of Placental Ribonuclease Inhibitor in complex with Human Eosinophil Derived Neurotoxin at 2A resolution
Keywords keywords	;HYDROLASE/INHIBITOR, COMPLEX (INHIBITOR-NUCLEASE), RIBONUCLEASE INHIBITOR, EOSINOPHIL DERIVED NEUROTOXIN, RNASE 2, LUECINE-RICH REPEATS, PROTEIN-PROTEIN INTERACTION, MOLECULAR RECOGNITION, HYDROLASE-INHIBITOR complex ;; HYDROLASE/INHIBITOR
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

2bex__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2bex__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2bex__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	25.72 Å
Rg (electron density)	24.75 Å
Total Rg	25.51 Å
Atom count	4458
Residues	591
Excluded volume	79128 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2bex__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2bex__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	RIBONUCLEASE INHIBITOR
Molecular weight formula_weight	49887.2 kDa
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	9505

SLDIQSLDIQCEELSDARWAELLPLLQQCQVVRLDDCGLTEARCKDISSALRVNPALAELNLRSNELGDVGVHCVLQGLQTPSCKIQKLSLQNCCLTGAGCGVLSSTLRTLPTLQELHLSDNLLGDAGLQLLCEGLLDPQCRLEKLQLEYCSLSAASCEPLASVLRAKPDFKELTVSNNDINEAGVRVLCQGLKDSPCQLEALKLESCGVTSDNCRDLCGIVASKASLRELALGSNKLGDVGMAELCPGLLHPSSRLRTLWIWECGITAKGCGDLCRVLRAKESLKELSLAGNELGDEGARLLCETLLEPGCQLESLWVKSCSFTAACCSHFSSVLAQNRFLLELQISNNRLEDAGVRELCQGLGQPGSVLRVLWLADCDVSDSSCSSLAATLLANHSLRELDLSNNCLGDAGILQLVESVRQPGCLLEQLVLYDIYWSEEMEDRLQALEKDKPSLRVIS

Entity 2 Entity 2 polymer

Description description	NONSECRETORY RIBONUCLEASE
Molecular weight formula_weight	15611.8 kDa
EC 编号 ec_number	3.1.27.5
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

MKPPQFTWAQWFETQHINMTSQQCTNAMQVINNYQRRCKNQNTFLLTTFANVVNVCGNPNMTCPSNKTRKNCHHSGSQVPLIHCNLTTPSPQNISNCRYAQTPANMFYIVACDNRDQRRDPPQYPVVPVHLDRII

Source Source

Source organism organism	HOMO SAPIENS
Common name common_name	HUMAN
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	ESCHERICHIA COLI

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	ALPHA-KETOMALONIC ACID
Molecular weight formula_weight	118.0 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	616

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d2bexa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Superfamily Superfamily superfamily	c.10.1 — RNI-like
Family Family family	c.10.1.1 — 28-residue LRR

Domain ID domain_id	d2bexb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Superfamily Superfamily superfamily	c.10.1 — RNI-like
Family Family family	c.10.1.1 — 28-residue LRR

Domain ID domain_id	d2bexc2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.5 — RNase A-like
Superfamily Superfamily superfamily	d.5.1 — RNase A-like
Family Family family	d.5.1.1 — Ribonuclease A-like

Domain ID domain_id	d2bexc3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2bexd2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.5 — RNase A-like
Superfamily Superfamily superfamily	d.5.1 — RNase A-like
Family Family family	d.5.1.1 — Ribonuclease A-like

Domain ID domain_id	d2bexd3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id	2bexA00
Class class	3 — Alpha Beta
Architecture architecture	80 — Alpha-Beta Horseshoe
Topology topology	10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Homologous superfamily homologous superfamily	10 — Ribonuclease Inhibitor

Domain ID domain_id	2bexB00
Class class	3 — Alpha Beta
Architecture architecture	80 — Alpha-Beta Horseshoe
Topology topology	10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Homologous superfamily homologous superfamily	10 — Ribonuclease Inhibitor

Domain ID domain_id	2bexC00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	130 — P-30 Protein
Homologous superfamily homologous superfamily	10 — Ribonuclease A-like domain

Domain ID domain_id	2bexD00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	130 — P-30 Protein
Homologous superfamily homologous superfamily	10 — Ribonuclease A-like domain

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Unit-cell length a length_a	91.980 Å
Unit-cell length b length_b	91.980 Å
Unit-cell length c length_c	257.650 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 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	1.990 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.2059
R_work r_work	0.2059
R_free r_free	0.2433

Crystal structure of Placental Ribonuclease Inhibitor in complex with Human Eosinophil Derived Neurotoxin at 2A resolution

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

RIBONUCLEASE INHIBITOR

State in the Current Structure

Other States of the Same Protein in the Database

NONSECRETORY RIBONUCLEASE

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2bex__assembly_1__model_1

2bex__assembly_1__model_1 | I(q)

2bex__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of Placental Ribonuclease Inhibitor in complex with Human Eosinophil Derived Neurotoxin at 2A resolution

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

RIBONUCLEASE INHIBITOR

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

NONSECRETORY RIBONUCLEASE

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2bex__assembly_1__model_1

2bex__assembly_1__model_1 | I(q)

2bex__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

CATH v4.4 (4 domains)

7. Citations (1)