8db2

Q108K:K40L:T51C:T53A:R58L:Q38F mutant of hCRBPII bound to synthetic fluorophore CM1V

Method: X-RAY DIFFRACTION Dmax: 47.8 Å Quality: GOOD

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

Retinol-binding protein 2

Homo sapiens

UniProt P50120

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 2–134 Mutation:Q108K,K40L,T51C,T53A,R58L,Q38F RH6 (2E)-3-[7-(diethylamino)-2-oxo-2H-1-benzopyran-3-yl]prop-2-enal, bound form × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4;297 K;PEG 4000, Ammonium Acetate, Sodium Acetate, pH 4.0 - 4.8 Resolution 1.50 Å R-free 0.268

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.

101 other PDB entries and 200 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RET2_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–133; UniProt 2–134

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.

SAXS scattering curve SAXS Profile

SAXS profile for 8db2

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8db2
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id8db2
Deposition date deposition_date2022-06-14
Structure title titleQ108K:K40L:T51C:T53A:R58L:Q38F mutant of hCRBPII bound to synthetic fluorophore CM1V
Keywords keywordshCRBPII, TRANSPORT PROTEIN; TRANSPORT PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier15.40
Radius of gyration Rg (electron density) rg_electron14.04
Forward intensity I(0) i04824340.00
Molecular weight molecular_weight15745.0 kDa
Excluded volume excluded_volume19701 ų
Envelope volume envelope_volume21598 ų
Hydration-shell volume shell_volume12954 ų
Envelope diameter envelope_diameter45.6
Shell Rg shell_rg20.00
Envelope Rg envelope_rg14.25
Shape Rg shape_rg14.02
Total Rg total_rg15.26
Total atoms total_atoms1109
Residues n_residues133
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

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

Maximum dimension Dmax dmax47.8
Rg (real space) rg_real15.28
Rg uncertainty (real space) rg_real_error0.24
I(0) (real space) i0_real4.8240e+06
I(0) uncertainty (real space) i0_real_error5.5550e+04
Rg (reciprocal space) rg_reciprocal15.30
I(0) (reciprocal space) i0_reciprocal4824000.0000
Solution quality estimate total_estimate0.8958
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary46.5
Skewness Skewness skewness0.066
Kurtosis Kurtosis kurtosis-0.434
Angular range angular_range— – 0.5000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha917400.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.890; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.986

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id8db2A01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology128 — Lipocalin
Homologous superfamily homologous superfamily20 — Calycin beta-barrel core domain

8. Citations (1)

9. Files and Curves (10)