SAXSdb — 2m5i

▼

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

BH3-interacting domain death agonist

Homo sapiens

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 61–195	Not recorded	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 6.6；318 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR sample composition：0.5 mM [U-15N] tBid in LPPG micelle, 0.8 mM [U-13C; U-15N] tBid in LPPG micelle, 0.8 mM [U-100% 15N; U-80% 2H] tBid in LPPG micelle, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition：1.0 mM [U-100% 13C; U-100% 15N] tBid in LPPG micelle, 100% D2O \| 100% D2O	Resolution not provided

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 2M5I	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1ZY3 Structural model of complex of Bcl-w protein with Bid BH3-peptide Deposited 2005-06-09	Different construct Different mutation/modification Different oligomeric state Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 82–101（20 aa）	Mutation：R203K	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；303 K；Ionic strength (raw mmCIF value) 10 mM NaCl；Pressure 1 NMR sample composition 0.7 mM Bcl-w U-15N,13C, 0.7 mM Bid BH3-peptide, 20 mM phosphate buffer, 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 0.7 mM Bcl-w U-15N, 0.7 mM Bid BH3-peptide, 20 mM phosphate buffer, 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 0.7 mM Bid BH3-peptide U-15N, 0.7 mM Bcl-w, 20 mM phosphate buffer, 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2BID HUMAN PRO-APOPTOTIC PROTEIN BID Deposited 1999-01-27	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–195（195 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Pressure 1	Resolution not provided
2KBW Solution Structure of human Mcl-1 complexed with human Bid_BH3 peptide Deposited 2008-12-09	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 76–106（31 aa） Fragment：BH3 motif, residues 76-106	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；303 K；Ionic strength (raw mmCIF value) 20；Pressure ambient NMR sample composition 0.5 mM [U-95% 15N] Mcl-1-1, 0.5 mM Bid_BH3-2, 20 mM HEPES-3, 1 mM DTT-4, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 mM Mcl-1-5, 0.5 mM [U-95% 15N] Bid_BH3-6, 20 mM HEPES-7, 1 mM DTT-8, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 mM [U-95% 13C; U-95% 15N] Mcl-1-9, 0.5 mM Bid_BH3-10, 20 mM HEPES-11, 1 mM DTT-12, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 mM [U-95% 13C; U-95% 15N] Mcl-1-13, 0.5 mM Bid_BH3-14, 20 mM HEPES-15, 1 mM DTT-16, 100 % [U-100% 2H] D2O-17, 100% D2O \| 100% D2O NMR sample composition 0.5 mM Mcl-1-18, 0.5 mM [U-95% 13C; U-95% 15N] Bid_BH3-19, 20 mM HEPES-20, 1 mM DTT-21, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 mM Mcl-1-22, 0.5 mM [U-95% 13C; U-95% 15N] Bid_BH3-23, 20 mM HEPES-24, 1 mM DTT-25, 100 % [U-100% 2H] D2O-26, 100% D2O \| 100% D2O NMR sample composition 0.4 mM [U-95% 15N] Mcl-1-27, 0.4 mM Bid_BH3-28, 20 mM HEPES-29, 1 mM DTT-30, 6 mg/mL Pf1 phage-31, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.4 mM Mcl-1-32, 0.4 mM [U-95% 15N] Bid_BH3-33, 20 mM HEPES-34, 1 mM DTT-35, 8 mg/mL Pf1 phage-36, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
4BD2 Bax domain swapped dimer in complex with BidBH3 Deposited 2012-10-04	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 76–109（34 aa） Fragment：RESIDUES 76-109	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 1.4 M SODIUM CITRATE, 0.1 M SODIUM CACODYLATE PH 5.75	Resolution 2.21 Å R-free 0.227
4QVE Crystal structure of Bcl-xL in complex with BID BH3 domain Deposited 2014-07-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 76–109（34 aa） Fragment：BID BH3, UNP RESIDUES 76-109	Not recorded	IMD IMIDAZOLE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10.5；291 K；2.0M Ammonium Sulphate, 0.2M Lithium Sulphate, 0.1M CAPS pH 10.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.05 Å R-free 0.224
4ZEQ Crystal Structure of human BFL-1 in complex with tBid BH3 peptide, Northeast Structural Genomics Consortium Target HX9247 Deposited 2015-04-20	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 125–150（26 aa） Fragment：UNP Residues 125-150	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；295 K；Sodium Malonate	Resolution 1.80 Å R-free 0.239
4ZIG Crystal Structure of core/latch dimer of Bax in complex with BidBH3mini Deposited 2015-04-28	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 125–144（20 aa） Fragment：BH3 motif	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；Tri-sodium citrate, Sodium cacodylate	Resolution 2.20 Å R-free 0.229
4ZII Crystal Structure of core/latch dimer of BaxI66A in complex with BidBH3 Deposited 2015-04-28	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 122–155（34 aa） Fragment：BH3 motif	Not recorded	EDO 1,2-ETHANEDIOL × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；Tri-sodium citrate, sodium cacodylate	Resolution 2.19 Å R-free 0.223
5AJJ Crystal structure of variola virus virulence factor F1L in complex with human Bid BH3 domain Deposited 2015-02-25	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 79–112（34 aa） Fragment：UNP RESIDUES 79-112	Not recorded	GOL GLYCEROL × 2 ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；1.8 M SODIUM ACETATE AND 0.1 M HEPES PH 6.5	Resolution 1.75 Å R-free 0.208
7M5A Crystal Structure of human BAK in complex with W3W5_BID Deposited 2021-03-23	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 80–100（21 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；293 K；0.2 M Potassium Sodium tartrate, 20% PEG 3350	Resolution 1.50 Å R-free 0.219
7M5B Crystal Structure of human BAK in complex with M3W5_BID Deposited 2021-03-23	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 80–100（21 aa）	Not recorded	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6.5；293 K；15% PEG 4000 0.2 M NaCl 0.1 MES 6.5	Resolution 1.85 Å R-free 0.205
7M5B Crystal Structure of human BAK in complex with M3W5_BID Deposited 2021-03-23	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 80–100（21 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6.5；293 K；15% PEG 4000 0.2 M NaCl 0.1 MES 6.5	Resolution 1.85 Å R-free 0.205
7P33 Epstein-Barr virus encoded Bcl-2 homolog BHRF-1 in complex with Bid BH3 peptide Deposited 2021-07-07	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 76–109（34 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.4M Ammonium phosphate mono basic	Resolution 2.79 Å R-free 0.274
7P33 Epstein-Barr virus encoded Bcl-2 homolog BHRF-1 in complex with Bid BH3 peptide Deposited 2021-07-07	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 76–109（34 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.4M Ammonium phosphate mono basic	Resolution 2.79 Å R-free 0.274
7P33 Epstein-Barr virus encoded Bcl-2 homolog BHRF-1 in complex with Bid BH3 peptide Deposited 2021-07-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 76–109（34 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.4M Ammonium phosphate mono basic	Resolution 2.79 Å R-free 0.274
7P33 Epstein-Barr virus encoded Bcl-2 homolog BHRF-1 in complex with Bid BH3 peptide Deposited 2021-07-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 76–109（34 aa）	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.4M Ammonium phosphate mono basic	Resolution 2.79 Å R-free 0.274
7P33 Epstein-Barr virus encoded Bcl-2 homolog BHRF-1 in complex with Bid BH3 peptide Deposited 2021-07-07	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain J 76–109（34 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.4M Ammonium phosphate mono basic	Resolution 2.79 Å R-free 0.274
7QTW Kaposi sarcoma associated herpes virus(KSHV) encoded apoptosis inhibitor, KsBcl-2 in complex with Bid BH3 Deposited 2022-01-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 76–109（34 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；0.1 M Sodium acetate pH 4.6 8% PEG 4000	Resolution 1.41 Å R-free 0.215

13 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	BID_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–135； UniProt 61–195

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	2m5i
Deposition date deposition_date	2013-02-25
Structure title title	NMR structures of human apoptotic protein tBid in LPPG micelle
Keywords keywords	tBid, apoptosis, membrane protein, LPPG micelle; MEMBRANE PROTEIN
Experimental Method method	SOLUTION NMR

▼

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

Radius of gyration Rg (Guinier) rg_guinier	29.22 Å
Radius of gyration Rg (electron density) rg_electron	29.41 Å
Forward intensity I(0) i0	1471420000.00
Molecular weight molecular_weight	304450.0 kDa
Excluded volume excluded_volume	375010 Å³
Envelope volume envelope_volume	113880 Å³
Hydration-shell volume shell_volume	32320 Å³
Envelope diameter envelope_diameter	108.3 Å
Shell Rg shell_rg	36.08 Å
Envelope Rg envelope_rg	29.97 Å
Shape Rg shape_rg	29.40 Å
Total Rg total_rg	29.58 Å
Total atoms total_atoms	43000
Residues n_residues	2700
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	100.2 Å
Rg (real space) rg_real	29.27 Å
Rg uncertainty (real space) rg_real_error	1.02 Å
I(0) (real space) i0_real	1.4710e+09
I(0) uncertainty (real space) i0_real_error	2.2410e+07
Rg (reciprocal space) rg_reciprocal	29.25 Å
I(0) (reciprocal space) i0_reciprocal	1471000000.0000
Solution quality estimate total_estimate	0.7049
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	35.2 Å
Skewness Skewness skewness	0.171
Kurtosis Kurtosis kurtosis	-0.584
Angular range angular_range	— – 0.2700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	344000.0000
Real-space data points n_real_points	55
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.884; Stabil: 1.000; Sysdev: 0.218; Positv: 1.000; Valcen: 0.929; Smooth: 0.925

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (1)

▶

8. Citations (1)

▶

Description description	BH3-interacting domain death agonist
Molecular weight formula_weight	15243.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	43000

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/m5/2m5i/2m5i.fit
pddf	/app/data/pr_computation/m5/2m5i/2m5i.pr.out
profile	/app/data/saxs_computation/m5/2m5i/2m5i.dat

NMR structures of human apoptotic protein tBid in LPPG micelle

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

BH3-interacting domain death agonist

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)