4x5x

HLA-DR1 mutant bN82A with covalently linked CLIP106-120(M107W)

Method: X-RAY DIFFRACTION Dmax: 115.5 Å Quality: REASONABLE

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

HLA class II histocompatibility antigen, DR alpha chain

Homo sapiens

UniProt P01903

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 26–217 Fragment:extracellular, UNP residues 26-217 HLA class II histocompatibility antigen, DRB1-1 beta chain × 1 (P04229) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;298 K;0.2M Sodium nitrate, 20% w/v PEG 3350, 0.1M Bis Tris propane pH 7.5 Resolution 3.20 Å R-free 0.262
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 26–217 Fragment:extracellular, UNP residues 26-217 HLA class II histocompatibility antigen, DRB1-1 beta chain × 1 (P04229) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;298 K;0.2M Sodium nitrate, 20% w/v PEG 3350, 0.1M Bis Tris propane pH 7.5 Resolution 3.20 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.

139 other PDB entries and 218 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DRA_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–193; UniProt 26–217 Author chain C; PDBConstruct 2–193; UniProt 26–217

HLA class II histocompatibility antigen, DRB1-1 beta chain

Homo sapiens

UniProt P04229

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 30–227 Fragment:extracellular, UNP residues 30-227 Mutation:N82A HLA class II histocompatibility antigen, DR alpha chain × 1 (P01903) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;298 K;0.2M Sodium nitrate, 20% w/v PEG 3350, 0.1M Bis Tris propane pH 7.5 Resolution 3.20 Å R-free 0.262
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 30–227 Fragment:extracellular, UNP residues 30-227 Mutation:N82A HLA class II histocompatibility antigen, DR alpha chain × 1 (P01903) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;298 K;0.2M Sodium nitrate, 20% w/v PEG 3350, 0.1M Bis Tris propane pH 7.5 Resolution 3.20 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.

48 other PDB entries and 82 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name 2B11_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 32–229; UniProt 30–227 Author chain D; PDBConstruct 32–229; UniProt 30–227

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 4x5x

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4x5x
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4x5x
Deposition date deposition_date2014-12-06
Structure title titleHLA-DR1 mutant bN82A with covalently linked CLIP106-120(M107W)
Keywords keywordsMHC II, IMMUNE SYSTEM, SELF ANTIGEN, INVARIANT CHAIN, CLIP; IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier34.08
Radius of gyration Rg (electron density) rg_electron33.54
Forward intensity I(0) i0116756000.00
Molecular weight molecular_weight86791.0 kDa
Excluded volume excluded_volume108660 ų
Envelope volume envelope_volume147950 ų
Hydration-shell volume shell_volume37690 ų
Envelope diameter envelope_diameter126.2
Shell Rg shell_rg39.81
Envelope Rg envelope_rg32.69
Shape Rg shape_rg33.50
Total Rg total_rg34.17
Total atoms total_atoms6130
Residues n_residues752
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 dmax115.5
Rg (real space) rg_real34.13
Rg uncertainty (real space) rg_real_error1.10
I(0) (real space) i0_real1.1680e+08
I(0) uncertainty (real space) i0_real_error2.1310e+06
Rg (reciprocal space) rg_reciprocal34.10
I(0) (reciprocal space) i0_reciprocal116800000.0000
Solution quality estimate total_estimate0.6767
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary32.6
Skewness Skewness skewness0.307
Kurtosis Kurtosis kurtosis-0.595
Angular range angular_range— – 0.2300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha16380000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.856; Stabil: 1.000; Sysdev: 0.122; Positv: 1.000; Valcen: 0.953; Smooth: 0.905

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id4x5xA01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Homologous superfamily homologous superfamily10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Domain ID domain_id4x5xA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4x5xB01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Homologous superfamily homologous superfamily10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Domain ID domain_id4x5xB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4x5xC01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Homologous superfamily homologous superfamily10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Domain ID domain_id4x5xC02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4x5xD01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology320 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Homologous superfamily homologous superfamily10 — Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1
Domain ID domain_id4x5xD02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)