4no5

Crystal structure of non-phosphorylated form of AMPD2 phosphopeptide bound to HLA-A2

Method: X-RAY DIFFRACTION Dmax: 75.7 Å Quality: EXCELLENT

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

HLA class I histocompatibility antigen, A-2 alpha chain

Homo sapiens

UniProt P01892

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 25–299 Fragment:extracellular domain (UNP residues 25-299) Beta-2-microglobulin × 1 (P61769) AMP deaminase 2 × 1 (Q01433) EDO 1,2-ETHANEDIOL × 3 NA SODIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;298 K;19% PEG3350, 0.1 M Bis-Tris propane, 0.1 M sodium tartrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.10 Å R-free 0.237

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.

271 other PDB entries and 465 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name 1A02_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–275; UniProt 25–299

Beta-2-microglobulin

Homo sapiens

UniProt P61769

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain B; UniProt 22–119 Fragment:UNP residues 22-119 HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) AMP deaminase 2 × 1 (Q01433) EDO 1,2-ETHANEDIOL × 3 NA SODIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;298 K;19% PEG3350, 0.1 M Bis-Tris propane, 0.1 M sodium tartrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.10 Å R-free 0.237

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.

1313 other PDB entries and 1998 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name B2MG_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–98; UniProt 22–119

AMP deaminase 2

OrganismNot specified

UniProt Q01433

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain C; UniProt 165–173 Fragment:peptide (UNP residues 165-173) HLA class I histocompatibility antigen, A-2 alpha chain × 1 (P01892) Beta-2-microglobulin × 1 (P61769) EDO 1,2-ETHANEDIOL × 3 NA SODIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;298 K;19% PEG3350, 0.1 M Bis-Tris propane, 0.1 M sodium tartrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.10 Å R-free 0.237

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.

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

View Construct and Data Evidence
UniProt name AMPD2_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–9; UniProt 165–173

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 4no5

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4no5
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4no5
Deposition date deposition_date2013-11-19
Structure title titleCrystal structure of non-phosphorylated form of AMPD2 phosphopeptide bound to HLA-A2
Keywords keywords;Nonphosphorylated peptide, peptide-MHC complex, MHC, peptide conformation, tumor immunology, post translational modification, tumor antigens, IMMUNE SYSTEM-ANTIGEN complex ;; IMMUNE SYSTEM/ANTIGEN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier24.21
Radius of gyration Rg (electron density) rg_electron23.02
Forward intensity I(0) i036429400.00
Molecular weight molecular_weight44714.0 kDa
Excluded volume excluded_volume55123 ų
Envelope volume envelope_volume67787 ų
Hydration-shell volume shell_volume24655 ų
Envelope diameter envelope_diameter78.9
Shell Rg shell_rg29.83
Envelope Rg envelope_rg23.15
Shape Rg shape_rg23.00
Total Rg total_rg23.90
Total atoms total_atoms3157
Residues n_residues382
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 dmax75.7
Rg (real space) rg_real24.15
Rg uncertainty (real space) rg_real_error0.44
I(0) (real space) i0_real3.6430e+07
I(0) uncertainty (real space) i0_real_error4.8120e+05
Rg (reciprocal space) rg_reciprocal24.16
I(0) (reciprocal space) i0_reciprocal36430000.0000
Solution quality estimate total_estimate0.9110
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.6
Skewness Skewness skewness0.256
Kurtosis Kurtosis kurtosis-0.464
Angular range angular_range— – 0.3300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9072000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.948; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.997

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id4no5A01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
Homologous superfamily homologous superfamily10 — MHC class I-like antigen recognition-like
Domain ID domain_id4no5A02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4no5B00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)