- PDB-4d8p: Structural and functional studies of the trans-encoded HLA-DQ2.3 ... -
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Basic information
Entry
Database: PDB / ID: 4d8p
Title
Structural and functional studies of the trans-encoded HLA-DQ2.3 (DQA1*03:01/DQB1*02:01) molecule
Components
HLA-DQA1 protein
Peptide from Gamma-gliadin,HLA class II histocompatibility antigen, DQ beta 1 chain
Keywords
IMMUNE SYSTEM / class II MHC
Function / homology
Function and homology information
nutrient reservoir activity / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / MHC class II protein complex / adaptive immune response / endosome membrane / lysosomal membrane / metal ion binding Similarity search - Function
Gliadin/LMW glutenin / Cys-rich Gliadin N-terminal / Plant lipid transfer protein / seed storage protein / trypsin-alpha amylase inhibitor domain family / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain ...Gliadin/LMW glutenin / Cys-rich Gliadin N-terminal / Plant lipid transfer protein / seed storage protein / trypsin-alpha amylase inhibitor domain family / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Roll / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta Similarity search - Domain/homology
HLA class II histocompatibility antigen DQ alpha chain / HLA class II histocompatibility antigen DQ beta chain / Gamma-gliadin Similarity search - Component
Biological species
Homo sapiens (human) Triticum aestivum (bread wheat)
#62 - Feb 2005 Major Histocompatibility Complex similarity (7)
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Assembly
Deposited unit
A: HLA-DQA1 protein B: Peptide from Gamma-gliadin,HLA class II histocompatibility antigen, DQ beta 1 chain C: HLA-DQA1 protein D: Peptide from Gamma-gliadin,HLA class II histocompatibility antigen, DQ beta 1 chain hetero molecules
Resolution: 3.05→29.31 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.897 / SU B: 55.62 / SU ML: 0.441 / Cross valid method: THROUGHOUT / ESU R Free: 0.479 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.28321
1086
5 %
RANDOM
Rwork
0.21045
-
-
-
obs
0.21398
20626
100 %
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all
-
21713
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-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 91.852 Å2
Baniso -1
Baniso -2
Baniso -3
1-
4.86 Å2
0 Å2
-9.39 Å2
2-
-
-1.81 Å2
0 Å2
3-
-
-
-7.39 Å2
Refinement step
Cycle: LAST / Resolution: 3.05→29.31 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
6102
0
12
6
6120
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.011
0.022
6286
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.393
1.944
8573
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
7.363
5
745
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
35.636
23.812
320
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
20.733
15
990
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
15.752
15
46
X-RAY DIFFRACTION
r_chiral_restr
0.09
0.2
938
X-RAY DIFFRACTION
r_gen_planes_refined
0.007
0.021
4892
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
0.552
1.5
3777
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
1.03
2
6178
X-RAY DIFFRACTION
r_scbond_it
1.047
3
2509
X-RAY DIFFRACTION
r_scangle_it
1.864
4.5
2395
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 3.05→3.129 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.416
81
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Rwork
0.382
1530
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obs
-
-
100 %
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
0.7577
0.7196
-0.3124
1.1959
-1.6204
3.6345
-0.2598
-0.1698
-0.1014
0.1723
-0.0675
0.2385
-0.7809
-0.0657
0.3273
0.1717
0.0231
0.023
0.1864
-0.0597
0.2721
12.4539
10.7449
52.4295
2
-0.1295
1.1057
1.1215
1.6354
-0.0299
2.5265
0.1095
0.0467
-0.0038
-0.2252
0.0806
0.0348
0.5066
0.3329
-0.1901
0.1317
0.0886
0.0546
0.2189
0.0671
0.1849
19.7702
-2.176
44.6958
3
0.1081
-1.1093
1.3584
2.461
-1.7963
3.7578
0.022
-0.3458
-0.098
-0.3609
-0.0098
0.2914
-0.1213
-0.6568
-0.0122
0.0576
-0.0177
-0.0062
0.3024
-0.1197
0.2272
-9.4289
-3.25
24.132
4
0.5589
0.5515
0.0006
1.083
-0.9771
2.2519
0.0335
0.0342
-0.059
-0.0442
-0.1148
-0.0451
0.0391
0.1246
0.0813
0.142
-0.0135
0.0102
0.1586
-0.0139
0.1594
6.9284
-5.5937
21.0325
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
1 - 182
2
X-RAY DIFFRACTION
2
B
3 - 190
3
X-RAY DIFFRACTION
3
C
1 - 181
4
X-RAY DIFFRACTION
4
D
3 - 190
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