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2l7w

Solution structure of the human Raf-1 kinase inhibitor protein

Method: SOLUTION NMR Dmax: 46.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Phosphatidylethanolamine-binding protein 1

Homo sapiens

UniProt P30086

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 1–187 Not recorded No other associated polymer SOLUTION NMR NMR measurement conditions：pH 4；298 K；Ionic strength (raw mmCIF value) 200 NMR sample composition：3mM [U-100% 13C; U-100% 15N] Raf-1 kinase inhibitor protein; 90% H2O/10% D2O | 90% H2O/10% D2O Resolution not provided

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 2L7W Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BD9 HUMAN PHOSPHATIDYLETHANOLAMINE BINDING PROTEIN Deposited 1998-05-12 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–186（186 aa）
Chain B 1–186（186 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；PROTEIN WAS CRYSTALLIZED FROM 28-32% PEG 4000/6000/8000, 200-300 MM SODIUM ACETATE, 100MM SODIUM CACODYLATE, PH 6.5; THEN SOAKED IN 28-32% PEG 4000/6000/8000, 200-300 MM SODIUM ACETATE, 100MM BIS-TRIS, PH 6.5.
Resolution 2.05 Å R-free 0.232
1BEH HUMAN PHOSPHATIDYLETHANOLAMINE BINDING PROTEIN IN COMPLEX WITH CACODYLATE Deposited 1998-05-14 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–186（186 aa）
Not recorded CAC CACODYLATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；PROTEIN WAS CRYSTALLIZED FROM 28-32% PEG 4000/6000/8000, 200-300 MM SODIUM ACETATE, 100MM SODIUM CACODYLATE., pH 6.5
Resolution 1.75 Å R-free 0.286
1BEH HUMAN PHOSPHATIDYLETHANOLAMINE BINDING PROTEIN IN COMPLEX WITH CACODYLATE Deposited 1998-05-14 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–186（186 aa）
Not recorded CAC CACODYLATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；PROTEIN WAS CRYSTALLIZED FROM 28-32% PEG 4000/6000/8000, 200-300 MM SODIUM ACETATE, 100MM SODIUM CACODYLATE., pH 6.5
Resolution 1.75 Å R-free 0.286
2QYQ Human raf kinase inhibitor protein (rkip) in complex with o-phosphotyrosine Deposited 2007-08-15 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–187（187 aa）
Not recorded PTR O-PHOSPHOTYROSINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；Initial crystallisation: 32-34% PEG 4OOO or 8000, 0.2 M sodium acetate, 0.1 M sodium acetate pH 4.0. Complex formed by soaking in: 32% PEG 4OOO, 0.2 M sodium chloride, 0.1 M O-phosphotyrosine, 0.1 M hepes pH 7.0., VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 1.95 Å R-free 0.208

3 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PEBP1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–187； UniProt 1–187

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 2l7w

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2l7w
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2l7w
Deposition date deposition_date2010-12-24
Structure title titleSolution structure of the human Raf-1 kinase inhibitor protein
Keywords keywordsRaf-1 kinase inhibitor protein, Signaling Protein Inhibitor; Signaling Protein Inhibitor
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier15.60 Å
Radius of gyration Rg (electron density) rg_electron15.31 Å
Forward intensity I(0) i02422010000.00
Molecular weight molecular_weight421140.0 kDa
Excluded volume excluded_volume527250 ų
Envelope volume envelope_volume37636 ų
Hydration-shell volume shell_volume18372 ų
Envelope diameter envelope_diameter53.6 Å
Shell Rg shell_rg23.40 Å
Envelope Rg envelope_rg16.93 Å
Shape Rg shape_rg15.27 Å
Total Rg total_rg15.55 Å
Total atoms total_atoms59060
Residues n_residues3740
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax46.8 Å
Rg (real space) rg_real15.47 Å
Rg uncertainty (real space) rg_real_error0.18 Å
I(0) (real space) i0_real2.4220e+09
I(0) uncertainty (real space) i0_real_error2.2050e+07
Rg (reciprocal space) rg_reciprocal15.48 Å
I(0) (reciprocal space) i0_reciprocal2422000000.0000
Solution quality estimate total_estimate0.8987
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary21.9 Å
Skewness Skewness skewness0.025
Kurtosis Kurtosis kurtosis-0.478
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1254000.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.911; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.971
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd2l7wa_
Class classb — All beta proteins
Fold Fold foldb.17 — PEBP-like
Superfamily Superfamily superfamilyb.17.1 — PEBP-like
Family Family familyb.17.1.1 — Phosphatidylethanolamine binding protein

CATH v4.4 (1 domains)

Domain ID domain_id2l7wA00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology280 — Phosphatidylethanolamine-binding Protein
Homologous superfamily homologous superfamily10 — PEBP-like
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8. Citations (1)

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9. Files and Curves (10)