SAXSdb — 4flb

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

Regulation of nuclear pre-mRNA domain-containing protein 2

Homo sapiens

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 19–149	Not recorded	SO4 SULFATE ION × 4 PR PRASEODYMIUM ION × 4 UNX UNKNOWN LIGAND × 10	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 5.5；291 K；25% PEG-3350, 0.2M ammounium sulfate, 0.1M sodium cacodylate, praseodymium(III) acetate, pH 5.5, vapor diffusion, temperature 291K	Resolution 1.80 Å R-free 0.216

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 4FLB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9HM8 NMR solution structure of RPRD2 CTD-interacting domain and pS2,7 RNAPII CTD peptide. Deposited 2024-12-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 16–155（140 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 8；293.15 K；Ionic strength (raw mmCIF value) 100；Pressure 1 NMR sample composition 0.4 mM [U-100% 13C; U-100% 15N] RPRD2 CID, 1 mM pS2pS7 CTD, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
9IA7 NMR solution structure of RPRD2 CTD-interacting domain and pT4 RNAPII CTD peptide. Deposited 2025-02-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 16–155（140 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 8；293.15 K；Ionic strength (raw mmCIF value) 100；Pressure 1 NMR sample composition 0.5 mM [U-100% 13C; U-100% 15N] RPRD2 CID, 1.5 mM pT4 CTD, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RPRD2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–132； UniProt 19–149

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	4flb
Deposition date deposition_date	2012-06-14
Structure title title	CID of human RPRD2
Keywords keywords	structural genomics consortium, sgc, PROTEIN BINDING; PROTEIN BINDING
Experimental Method method	X-RAY DIFFRACTION

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

该条目暂无 SAXS 数据。

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

该条目暂无 P(r) 分析数据。

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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	Regulation of nuclear pre-mRNA domain-containing protein 2
Molecular weight formula_weight	16757.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1202

GSAGALESSLDRKFQSVTNTMESIQGLSSWCIENKKHHSTIVYHWMKWLRRSAYPHRLNLFYLANDVIQNCKRKNAIIFRESFADVLPEAAALVKDPSVSKSVERIFKIWEDRNVYPEEMIVALREALSTTFKTQKQLKENLNK

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	PRASEODYMIUM ION
Molecular weight formula_weight	140.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	UNKNOWN ATOM OR ION
Source method src_method	syn
Copy count entity_count	5

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	72

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d4flba_
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.9 — ENTH/VHS domain
Family Family family	a.118.9.0 — automated matches

CATH v4.4 (1 domains)

Domain ID domain_id	4flbA00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	90 —

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8. Citations (1)

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Unit-cell length a length_a	40.339 Å
Unit-cell length b length_b	40.339 Å
Unit-cell length c length_c	145.750 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 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	1.802 Å
Low-resolution limit resolution_low	28.540 Å
R factor r_factor	0.1770
R_work r_work	0.1746
R_free r_free	0.2162

CID of human RPRD2