SAXSdb — 2vm5

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

BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 1

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 141–244	Fragment：BIR2 DOMAIN, RESIDUES 141-244	ZN ZINC ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5；0.1M CITRIC ACID, PH 5, 20% PEG 6000	Resolution 1.80 Å R-free 0.220

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 2VM5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8FVU Cryo-EM structure of human Needle/NAIP/NLRC4 (R288A) Deposited 2023-01-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1403（1403 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	BIRC1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–106； UniProt 141–244

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2vm5
Deposition date deposition_date	2008-01-23
Structure title title	HUMAN BIR2 DOMAIN OF BACULOVIRAL INHIBITOR OF APOPTOSIS REPEAT- CONTAINING 1 (BIRC1)
Keywords keywords	APOPTOSIS; APOPTOSIS
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	16.38 Å
Radius of gyration Rg (electron density) rg_electron	15.96 Å
Forward intensity I(0) i0	3253080.00
Molecular weight molecular_weight	12276.0 kDa
Excluded volume excluded_volume	15208 Å³
Envelope volume envelope_volume	19506 Å³
Hydration-shell volume shell_volume	11316 Å³
Envelope diameter envelope_diameter	69.8 Å
Shell Rg shell_rg	20.64 Å
Envelope Rg envelope_rg	17.61 Å
Shape Rg shape_rg	15.95 Å
Total Rg total_rg	16.97 Å
Total atoms total_atoms	859
Residues n_residues	103
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

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

Maximum dimension Dmax dmax	44.6 Å
Rg (real space) rg_real	15.03 Å
Rg uncertainty (real space) rg_real_error	0.09 Å
I(0) (real space) i0_real	3.0860e+06
I(0) uncertainty (real space) i0_real_error	3.3200e+04
Rg (reciprocal space) rg_reciprocal	16.66 Å
I(0) (reciprocal space) i0_reciprocal	3253000.0000
Solution quality estimate total_estimate	0.6737
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	17.8 Å
Skewness Skewness skewness	0.419
Kurtosis Kurtosis kurtosis	-0.099
Angular range angular_range	— – 0.4850 Å⁻¹
Current regularization parameter α current_alpha	2.0910
Highest regularization parameter α highest_alpha	768000.0000
Real-space data points n_real_points	79
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.015; Oscil: 0.930; Stabil: 0.994; Sysdev: 0.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 1
Molecular weight formula_weight	12376.1 kDa
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	916

SMRVKNLKSRLRGGKMRYQEEEARLASFRNWPFYVQGISPCVLSEAGFVFTGKQDTVQCFSCGGCLGNWEEGDDPWKEHAKWFPKCEFLRSKKSSEEITQYIQSYK

来源 Source

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

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	51

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2vm5a1
Class class	g — Small proteins
Fold Fold fold	g.52 — Inhibitor of apoptosis (IAP) repeat
Superfamily Superfamily superfamily	g.52.1 — Inhibitor of apoptosis (IAP) repeat
Family Family family	g.52.1.0 — automated matches

Domain ID domain_id	d2vm5a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	2vm5A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1170 — Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A
Homologous superfamily homologous superfamily	10 — Inhibitor Of Apoptosis Protein (2mihbC-IAP-1); Chain A

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8. Citations (1)

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Unit-cell length a length_a	36.500 Å
Unit-cell length b length_b	43.100 Å
Unit-cell length c length_c	57.000 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	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1810
R_work r_work	0.1780
R_free r_free	0.2200

fit	/app/data/saxs_computation/vm/2vm5/2vm5.fit
pddf	/app/data/pr_computation/vm/2vm5/2vm5.pr.out
profile	/app/data/saxs_computation/vm/2vm5/2vm5.dat

HUMAN BIR2 DOMAIN OF BACULOVIRAL INHIBITOR OF APOPTOSIS REPEAT- CONTAINING 1 (BIRC1)

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

BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 1

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