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5e1t

Crystal structure of TRAF1 TRAF domain

Method: X-RAY DIFFRACTION Dmax: 91.2 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

TNF receptor-associated factor 1

Homo sapiens

UniProt Q13077

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 220–416 Chain B； UniProt 220–416 Chain C； UniProt 220–416 Fragment：UNP residues 220-416 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；298 K；(NH4)2SO4, NaCl Resolution 2.80 Å R-free 0.262

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 5E1T Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3M0D Crystal structure of the TRAF1:TRAF2:cIAP2 complex Deposited 2010-03-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 181–244（64 aa） Fragment：Residues 266-329
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；0.15M AmSO4, 0.1M MES, 15% PEG 4000, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.80 Å R-free 0.247
3M0D Crystal structure of the TRAF1:TRAF2:cIAP2 complex Deposited 2010-03-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 181–244（64 aa） Fragment：Residues 266-329
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；0.15M AmSO4, 0.1M MES, 15% PEG 4000, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.80 Å R-free 0.247
5H10 TRAF1-TANk complex Deposited 2016-10-07 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 220–416（197 aa）
Chain B 220–416（197 aa）
Chain C 220–416（197 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.38M Ammonium sulfate, 0.1M CHES pH 9.3, 200mM NaCl
Resolution 3.21 Å R-free 0.270

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

View Construct and Data Evidence
UniProt name TRAF1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–197； UniProt 220–416 Author chain B； PDBConstruct 1–197； UniProt 220–416 Author chain C； PDBConstruct 1–197； UniProt 220–416

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 5e1t

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5e1t
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5e1t
Deposition date deposition_date2015-09-30
Structure title titleCrystal structure of TRAF1 TRAF domain
Keywords keywordsProtein interaction domain, PROTEIN BINDING; PROTEIN BINDING
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier29.87 Å
Radius of gyration Rg (electron density) rg_electron28.82 Å
Forward intensity I(0) i068565000.00
Molecular weight molecular_weight65376.0 kDa
Excluded volume excluded_volume82182 ų
Envelope volume envelope_volume105990 ų
Hydration-shell volume shell_volume31422 ų
Envelope diameter envelope_diameter92.1 Å
Shell Rg shell_rg34.78 Å
Envelope Rg envelope_rg28.88 Å
Shape Rg shape_rg28.79 Å
Total Rg total_rg29.54 Å
Total atoms total_atoms4599
Residues n_residues569
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 dmax91.2 Å
Rg (real space) rg_real29.74 Å
Rg uncertainty (real space) rg_real_error0.57 Å
I(0) (real space) i0_real6.8570e+07
I(0) uncertainty (real space) i0_real_error1.1840e+06
Rg (reciprocal space) rg_reciprocal29.80 Å
I(0) (reciprocal space) i0_reciprocal68570000.0000
Solution quality estimate total_estimate0.9128
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary37.9 Å
Skewness Skewness skewness0.082
Kurtosis Kurtosis kurtosis-0.665
Angular range angular_range— – 0.2650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7360000.0000
Real-space data points n_real_points54
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.970; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.951
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id5e1tA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology210 — Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A
Homologous superfamily homologous superfamily10 — Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A
Domain ID domain_id5e1tB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology210 — Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A
Homologous superfamily homologous superfamily10 — Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A
Domain ID domain_id5e1tC00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology210 — Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A
Homologous superfamily homologous superfamily10 — Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A
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8. Citations (1)

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9. Files and Curves (10)