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2k89

Solution structure of a novel Ubiquitin-binding domain from Human PLAA (PFUC, Gly76-Pro77 cis isomer)

Method: SOLUTION NMR Dmax: 48.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Phospholipase A-2-activating protein

Homo sapiens

UniProt Q9Y263

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 386–465 Fragment：UNP residues 386-465 No other associated polymer SOLUTION NMR NMR measurement conditions：pH 6.5；298 K；Ionic strength (raw mmCIF value) 50mM NaCl；Pressure ambient NMR sample composition：1 mM [U-99% 13C; U-99% 15N] PFUC_cis, 90% H2O, 10% D2O | 90% H2O/10% D2O NMR sample composition：1 mM [U-99% 13C; U-99% 15N] PFUC_cis, 100% D2O | 100% 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 2K89 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2K8A Solution structure of a novel Ubiquitin-binding domain from Human PLAA (PFUC, Gly76-Pro77 trans isomer) Deposited 2008-09-04 Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 386–465（80 aa） Fragment：UNP residues 386-465
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 50mM NaCl；Pressure ambient
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] PFUC_trans, 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] PFUC_trans, 100% D2O | 100% D2O
Resolution not provided
2K8B Solution structure of PLAA family ubiquitin binding domain (PFUC) cis isomer in complex with ubiquitin Deposited 2008-09-04 Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 386–465（80 aa） Fragment：UNP residues 386-465
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 50mM NaCl；Pressure ambient
NMR sample composition 0.2 mM Ubiquitin, 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 0.2 mM PFUC_cis, 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
2K8C Solution structure of PLAA family ubiquitin binding domain (PFUC) trans isomer in complex with ubiquitin Deposited 2008-09-04 Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 386–465（80 aa） Fragment：UNP residues 386-465
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 50mM NaCl；Pressure ambient
NMR sample composition 0.2 mM [U-100% 15N] Ubiquitin, 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition 0.2 mM [U-100% 15N] PFUC_trans, 90% H2O, 10% D2O | 90% H2O/10% D2O
Resolution not provided
3EBB PLAP/P97 complex Deposited 2008-08-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 511–794（284 aa） Fragment：PUL DOMAIN, residues 511-795
Chain B 511–794（284 aa） Fragment：PUL DOMAIN, residues 511-795
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；30% PEG 4000, 0.1 M TRIS, PH 8.50, 0.2 M MGCL2, , VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.90 Å R-free 0.248
3EBB PLAP/P97 complex Deposited 2008-08-27 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 511–794（284 aa） Fragment：PUL DOMAIN, residues 511-795
Chain D 511–794（284 aa） Fragment：PUL DOMAIN, residues 511-795
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；30% PEG 4000, 0.1 M TRIS, PH 8.50, 0.2 M MGCL2, , VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.90 Å R-free 0.248

4 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PLAP_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–80； UniProt 386–465

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 2k89

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2k89
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2k89
Deposition date deposition_date2008-09-04
Structure title titleSolution structure of a novel Ubiquitin-binding domain from Human PLAA (PFUC, Gly76-Pro77 cis isomer)
Keywords keywordsUbiquitin binding, WD repeat, PROTEIN BINDING; PROTEIN BINDING
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier13.77 Å
Radius of gyration Rg (electron density) rg_electron13.17 Å
Forward intensity I(0) i0251504000.00
Molecular weight molecular_weight135330.0 kDa
Excluded volume excluded_volume169680 ų
Envelope volume envelope_volume27503 ų
Hydration-shell volume shell_volume14357 ų
Envelope diameter envelope_diameter52.1 Å
Shell Rg shell_rg22.14 Å
Envelope Rg envelope_rg17.14 Å
Shape Rg shape_rg13.12 Å
Total Rg total_rg13.64 Å
Total atoms total_atoms18690
Residues n_residues1200
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 dmax48.7 Å
Rg (real space) rg_real13.76 Å
Rg uncertainty (real space) rg_real_error0.36 Å
I(0) (real space) i0_real2.5150e+08
I(0) uncertainty (real space) i0_real_error2.7130e+06
Rg (reciprocal space) rg_reciprocal13.76 Å
I(0) (reciprocal space) i0_reciprocal251500000.0000
Solution quality estimate total_estimate0.8579
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary16.6 Å
Skewness Skewness skewness0.293
Kurtosis Kurtosis kurtosis-0.130
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha105600.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.736; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.959; Smooth: 0.983
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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) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id2k89A00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily870 — PFU (PLAA family ubiquitin binding), C-terminal domain
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8. Citations (1)

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9. Files and Curves (10)