SAXSdb — 6lt6

▼

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

MHC class I antigen

Macaca mulatta

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 22–297	Mutation：R128E, K177E	Beta-2-microglobulin × 1 （Q6V7J5） EKG (2R)-2,3-dihydroxypropyl hexadecanoate × 1 EDO 1,2-ETHANEDIOL × 8 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；0.1M Bis-Tris propane, 0.2M Sodium malonate dibasic monohydrate, 20% PEG3350	Resolution 2.15 Å R-free 0.232

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 6LT6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6IWG Crystal structure of rhesus macaque MHC class I molecule Mamu-B*05104 complexed with N-myristoylated 4-mer lipopeptide derived from SIV nef protein Deposited 2018-12-05	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 22–297（276 aa）	Mutation：R128E,K177E,D223E,K264E	NA SODIUM ION × 4 EDO 1,2-ETHANEDIOL × 18 BO3 BORIC ACID × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277.15 K；100mM MIB, 25% PEG 1500	Resolution 1.80 Å R-free 0.215
6IWH Crystal structure of rhesus macaque MHC class I molecule Mamu-B*05104 complexed with C14-GGGI lipopeptide Deposited 2018-12-05	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 22–297（276 aa）	Mutation：R128E,K177E,D223E,K264E	NA SODIUM ION × 5 EDO 1,2-ETHANEDIOL × 13	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；200mM Sodium fluoride, 100mM Bis-Tris propane, 20% PEG 3350	Resolution 1.95 Å R-free 0.217
7BYD Crystal structure of SN45 TCR in complex with lipopeptide-bound Mamu-B*05104 Deposited 2020-04-22	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 22–297（276 aa）	Mutation：R149E,K198E,D244E	IOD IODIDE ION × 9 EDO 1,2-ETHANEDIOL × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 CA CALCIUM ION × 1 MYR MYRISTIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.2 M sodium iodide, 0.1 M Bis-Tris-propane pH 6.5 and 20% PEG3350	Resolution 2.80 Å R-free 0.250
7BYD Crystal structure of SN45 TCR in complex with lipopeptide-bound Mamu-B*05104 Deposited 2020-04-22	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain F 22–297（276 aa）	Mutation：R149E,K198E,D244E	IOD IODIDE ION × 10 EDO 1,2-ETHANEDIOL × 3 MYR MYRISTIC ACID × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.2 M sodium iodide, 0.1 M Bis-Tris-propane pH 6.5 and 20% PEG3350	Resolution 2.80 Å R-free 0.250

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

View Construct and Data Evidence

UniProt name	B2ZHY7_MACMU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–276； UniProt 22–297

Beta-2-microglobulin

Macaca mulatta

UniProt Q6V7J5

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 20–119	Not recorded	MHC class I antigen × 1 （B2ZHY7） EKG (2R)-2,3-dihydroxypropyl hexadecanoate × 1 EDO 1,2-ETHANEDIOL × 8 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；0.1M Bis-Tris propane, 0.2M Sodium malonate dibasic monohydrate, 20% PEG3350	Resolution 2.15 Å R-free 0.232

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 6LT6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3JTT Cystal structure of Rhesus macaque MHC class I:Mamu-A*02 Deposited 2009-09-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 21–119（99 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.1 M Bis-Tris pH 5.5, 2 M ammonium sulfate , VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.80 Å R-free 0.255
3JTT Cystal structure of Rhesus macaque MHC class I:Mamu-A*02 Deposited 2009-09-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 21–119（99 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.1 M Bis-Tris pH 5.5, 2 M ammonium sulfate , VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.80 Å R-free 0.255
3JTT Cystal structure of Rhesus macaque MHC class I:Mamu-A*02 Deposited 2009-09-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 21–119（99 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；0.1 M Bis-Tris pH 5.5, 2 M ammonium sulfate , VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.80 Å R-free 0.255
3RWC Crystal structure of rhesus macaque MHC class I molecule Mamu-B*17-IW9 Deposited 2011-05-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 21–119（99 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å R-free 0.249
3RWC Crystal structure of rhesus macaque MHC class I molecule Mamu-B*17-IW9 Deposited 2011-05-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 21–119（99 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å R-free 0.249
3RWD rhesus macaque MHC class I molecule Mamu-B*17-IW11 Deposited 2011-05-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 21–119（99 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.60 Å R-free 0.277
3RWD rhesus macaque MHC class I molecule Mamu-B*17-IW11 Deposited 2011-05-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 21–119（99 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.60 Å R-free 0.277
3RWE rhesus macaque MHC class I molecule Mamu-B*17-FW9 Deposited 2011-05-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 21–119（99 aa）	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å R-free 0.251
3RWF Rhesus macaque MHC class I molecule Mamu-B*17-QW9 Deposited 2011-05-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 21–119（99 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.60 Å R-free 0.246
3RWG Rhesus macaque MHC class I molecule Mamu-B*17-MW9 Deposited 2011-05-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 21–119（99 aa）	Not recorded	XPE 3,6,9,12,15,18,21,24,27-NONAOXANONACOSANE-1,29-DIOL × 1 NA SODIUM ION × 1 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å R-free 0.237
3RWH Rhesus macaque MHC class I molecule Mamu-B*17-MF8 Deposited 2011-05-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 21–119（99 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.60 Å R-free 0.272
3RWH Rhesus macaque MHC class I molecule Mamu-B*17-MF8 Deposited 2011-05-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 21–119（99 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.60 Å R-free 0.272
3RWI Rhesus macaque MHC class I molecule Mamu-B*17-GW10 Deposited 2011-05-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 21–119（99 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.01 Å R-free 0.210
4ZFZ Crystal structure of rhesus macaque MHC class I molecule Mamu-B*098 complexed with myristoylated 5-mer lipopeptide derived from SIV Nef protein Deposited 2015-04-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 20–119（100 aa）	Not recorded	ZN ZINC ION × 6 EDO 1,2-ETHANEDIOL × 16 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 CL CHLORIDE ION × 1 MYR MYRISTIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；Zinc chloride, Tris-HCl, PEG6000	Resolution 1.76 Å R-free 0.228
4ZFZ Crystal structure of rhesus macaque MHC class I molecule Mamu-B*098 complexed with myristoylated 5-mer lipopeptide derived from SIV Nef protein Deposited 2015-04-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 20–119（100 aa）	Not recorded	ZN ZINC ION × 5 EDO 1,2-ETHANEDIOL × 15 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 MYR MYRISTIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；Zinc chloride, Tris-HCl, PEG6000	Resolution 1.76 Å R-free 0.228
4ZFZ Crystal structure of rhesus macaque MHC class I molecule Mamu-B*098 complexed with myristoylated 5-mer lipopeptide derived from SIV Nef protein Deposited 2015-04-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 20–119（100 aa）	Not recorded	ZN ZINC ION × 3 EDO 1,2-ETHANEDIOL × 16 CL CHLORIDE ION × 1 MYR MYRISTIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；Zinc chloride, Tris-HCl, PEG6000	Resolution 1.76 Å R-free 0.228
4ZFZ Crystal structure of rhesus macaque MHC class I molecule Mamu-B*098 complexed with myristoylated 5-mer lipopeptide derived from SIV Nef protein Deposited 2015-04-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain K 20–119（100 aa）	Not recorded	ZN ZINC ION × 4 EDO 1,2-ETHANEDIOL × 18 CL CHLORIDE ION × 1 MYR MYRISTIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；Zinc chloride, Tris-HCl, PEG6000	Resolution 1.76 Å R-free 0.228
6IWG Crystal structure of rhesus macaque MHC class I molecule Mamu-B*05104 complexed with N-myristoylated 4-mer lipopeptide derived from SIV nef protein Deposited 2018-12-05	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 20–119（100 aa）	Not recorded	NA SODIUM ION × 4 EDO 1,2-ETHANEDIOL × 18 BO3 BORIC ACID × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277.15 K；100mM MIB, 25% PEG 1500	Resolution 1.80 Å R-free 0.215
6IWH Crystal structure of rhesus macaque MHC class I molecule Mamu-B*05104 complexed with C14-GGGI lipopeptide Deposited 2018-12-05	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 20–119（100 aa）	Not recorded	NA SODIUM ION × 5 EDO 1,2-ETHANEDIOL × 13	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；200mM Sodium fluoride, 100mM Bis-Tris propane, 20% PEG 3350	Resolution 1.95 Å R-free 0.217
6LAH Crystal structure of rhesus macaque MHC class I molecule Mamu-B*098 complexed with lysophosphatidylcholine Deposited 2019-11-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 20–119（100 aa）	Not recorded	ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 12 EKG (2R)-2,3-dihydroxypropyl hexadecanoate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.4；293.15 K；Tris 0.1 M, 2 mM ZnCl2, PEG6000 13%	Resolution 1.87 Å R-free 0.230
6LAH Crystal structure of rhesus macaque MHC class I molecule Mamu-B*098 complexed with lysophosphatidylcholine Deposited 2019-11-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 20–119（100 aa）	Not recorded	ZN ZINC ION × 5 EDO 1,2-ETHANEDIOL × 19 EKG (2R)-2,3-dihydroxypropyl hexadecanoate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.4；293.15 K；Tris 0.1 M, 2 mM ZnCl2, PEG6000 13%	Resolution 1.87 Å R-free 0.230
6LAM Crystal structure of rhesus macaque MHC class I molecule Mamu-B*098 complexed with lysophosphatidylethanolamine Deposited 2019-11-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 20–119（100 aa）	Not recorded	ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 10 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 EKG (2R)-2,3-dihydroxypropyl hexadecanoate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.15；293.15 K；Tris 0.1 M, 2 mM ZnCl2, PEG6000 13%	Resolution 1.80 Å R-free 0.229
6LAM Crystal structure of rhesus macaque MHC class I molecule Mamu-B*098 complexed with lysophosphatidylethanolamine Deposited 2019-11-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 20–119（100 aa）	Not recorded	ZN ZINC ION × 4 EDO 1,2-ETHANEDIOL × 16 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 EKG (2R)-2,3-dihydroxypropyl hexadecanoate × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.15；293.15 K；Tris 0.1 M, 2 mM ZnCl2, PEG6000 13%	Resolution 1.80 Å R-free 0.229
6LB2 Crystal structure of rhesus macaque MHC class I molecule Mamu-B*098 complexed with mono-acyl glycerol Deposited 2019-11-13	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 20–119（100 aa）	Not recorded	ZN ZINC ION × 4 EDO 1,2-ETHANEDIOL × 22 EKG (2R)-2,3-dihydroxypropyl hexadecanoate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.7；293.15 K；Tris 0.1 M, 2 mM ZnCl2, PEG6000 13%	Resolution 1.69 Å R-free 0.227
6LB2 Crystal structure of rhesus macaque MHC class I molecule Mamu-B*098 complexed with mono-acyl glycerol Deposited 2019-11-13	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 20–119（100 aa）	Not recorded	ZN ZINC ION × 3 EDO 1,2-ETHANEDIOL × 19 EKG (2R)-2,3-dihydroxypropyl hexadecanoate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.7；293.15 K；Tris 0.1 M, 2 mM ZnCl2, PEG6000 13%	Resolution 1.69 Å R-free 0.227
7BYD Crystal structure of SN45 TCR in complex with lipopeptide-bound Mamu-B*05104 Deposited 2020-04-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 20–119（100 aa）	Not recorded	IOD IODIDE ION × 9 EDO 1,2-ETHANEDIOL × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 CA CALCIUM ION × 1 MYR MYRISTIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.2 M sodium iodide, 0.1 M Bis-Tris-propane pH 6.5 and 20% PEG3350	Resolution 2.80 Å R-free 0.250
7BYD Crystal structure of SN45 TCR in complex with lipopeptide-bound Mamu-B*05104 Deposited 2020-04-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain G 20–119（100 aa）	Not recorded	IOD IODIDE ION × 10 EDO 1,2-ETHANEDIOL × 3 MYR MYRISTIC ACID × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.2 M sodium iodide, 0.1 M Bis-Tris-propane pH 6.5 and 20% PEG3350	Resolution 2.80 Å R-free 0.250

15 other PDB entries and 27 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	B2MG_MACMU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–100； UniProt 20–119

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6lt6
Deposition date deposition_date	2020-01-21
Structure title title	Crystal structure of rhesus macaque MHC class I molecule Mamu-B*05104 complexed with lysophosphatidylcholine
Keywords keywords	MHC class I protein, complex, lysophospholipid, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	24.27 Å
Radius of gyration Rg (electron density) rg_electron	23.01 Å
Forward intensity I(0) i0	35443600.00
Molecular weight molecular_weight	44416.0 kDa
Excluded volume excluded_volume	54894 Å³
Envelope volume envelope_volume	67493 Å³
Hydration-shell volume shell_volume	24537 Å³
Envelope diameter envelope_diameter	79.2 Å
Shell Rg shell_rg	29.87 Å
Envelope Rg envelope_rg	23.18 Å
Shape Rg shape_rg	22.99 Å
Total Rg total_rg	23.87 Å
Total atoms total_atoms	3138
Residues n_residues	376
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	75.7 Å
Rg (real space) rg_real	24.20 Å
Rg uncertainty (real space) rg_real_error	0.50 Å
I(0) (real space) i0_real	3.5440e+07
I(0) uncertainty (real space) i0_real_error	5.0000e+05
Rg (reciprocal space) rg_reciprocal	24.22 Å
I(0) (reciprocal space) i0_reciprocal	35440000.0000
Solution quality estimate total_estimate	0.8334
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.1 Å
Skewness Skewness skewness	0.250
Kurtosis Kurtosis kurtosis	-0.464
Angular range angular_range	— – 0.3250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8007000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.946; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	MHC class I antigen
Molecular weight formula_weight	31905.1 kDa
Mutation mutation	R128E, K177E
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3396

GSHSLRYFGTAVSRPGRGEPRFIYVGYVDDTQFVRFDSDAASPRTEPRAPWVEQEGPEYWEEETRRAKARAQTDRADLRTLRGYYNQSEAGSHTLQWMAGCDLGPNGRLLRGYHQSAYDGKDYIALNEDLRSWIAADMAAQNTQRKWEATRYAERFRAYLEGPCLEWLRRYLENGKETLQHADPPKTHVTHHPVSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDIEFVETRPAGDGTFQKWGAVVVPSGEEQRYTCHVQHKGLPEPLTLRWEP

来源 Source

来源生物 organism	Macaca mulatta
通用名 common_name	Rhesus macaque
NCBI Class编号 ncbi_taxonomy_id	9544
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Beta-2-microglobulin
Molecular weight formula_weight	11731.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

AIQRTPKIQVYSRHPPENGKPNFLNCYVSGFHPSDIEVDLLKNGEKMGKVEHSDLSFSKDWSFYLLYYTEFTPNEKDEYACRVNHVTLSGPRTVKWDRDM

来源 Source

来源生物 organism	Macaca mulatta
通用名 common_name	Rhesus macaque
NCBI Class编号 ncbi_taxonomy_id	9544
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	(2R)-2,3-dihydroxypropyl hexadecanoate
Molecular weight formula_weight	330.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 5 Entity 5 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	208

▼

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d6lt6a1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.19 — MHC antigen-recognition domain
Superfamily Superfamily superfamily	d.19.1 — MHC antigen-recognition domain
Family Family family	d.19.1.1 — MHC antigen-recognition domain

Domain ID domain_id	d6lt6a2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d6lt6b_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (3 domains)

Domain ID domain_id	6lt6A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	500 — Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — MHC class I-like antigen recognition-like

Domain ID domain_id	6lt6A02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6lt6B00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

▶

8. Citations (1)

▶

Unit-cell length a length_a	54.451 Å
Unit-cell length b length_b	81.028 Å
Unit-cell length c length_c	106.108 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	2.150 Å
Low-resolution limit resolution_low	45.190 Å
R factor r_factor	0.1844
R_work r_work	0.1819
R_free r_free	0.2315

fit	/app/data/saxs_computation/lt/6lt6/6lt6.fit
pddf	/app/data/pr_computation/lt/6lt6/6lt6.pr.out
profile	/app/data/saxs_computation/lt/6lt6/6lt6.dat

Crystal structure of rhesus macaque MHC class I molecule Mamu-B*05104 complexed with lysophosphatidylcholine

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

MHC class I antigen

State in the Current Structure

Other States of the Same Protein in the Database

Beta-2-microglobulin

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)