SAXSdb — 8hu6

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

AMP deaminase 2

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 homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 211–879 Chain B； UniProt 211–879 Chain C； UniProt 211–879 Chain D； UniProt 211–879	Not recorded	ZN ZINC ION × 4 SO4 SULFATE ION × 4 AMP ADENOSINE MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.9；295.15 K；85 mM MES ph 5.9, 20% PEG8000, 170 mM ammonium sulfate, 15% glycerol, 10mM AMP	Resolution 2.33 Å R-free 0.268

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 8HU6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4NO3 Crystal structure of AMPD2 phosphopeptide bound to HLA-A2 Deposited 2013-11-19	Different construct 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 C 165–173（9 aa） Fragment：peptide (UNP residues 165-173)	Non-standard monomer：Yes (specific site not provided by mmCIF)	EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；12% PEG3350, 8% tacsimate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.70 Å R-free 0.232
4NO5 Crystal structure of non-phosphorylated form of AMPD2 phosphopeptide bound to HLA-A2 Deposited 2013-11-19	Different construct 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 C 165–173（9 aa） Fragment：peptide (UNP residues 165-173)	Not recorded	EDO 1,2-ETHANEDIOL × 3 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；19% PEG3350, 0.1 M Bis-Tris propane, 0.1 M sodium tartrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.10 Å R-free 0.237
8HUB AMP deaminase 2 in complex with an inhibitor Deposited 2022-12-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 211–879（669 aa） Chain B 211–879（669 aa） Chain C 211–879（669 aa） Chain D 211–879（669 aa）	Not recorded	ZN ZINC ION × 4 N4X 3,3-dimethyl-4-(phenylmethyl)-2~{H}-quinoxaline-1-carboxamide × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；295.15 K；85 mM MES ph 5.9, 20% PEG8000, 170 mM ammonium sulfate, 15% glycerol, 10mM compound	Resolution 3.25 Å R-free 0.276

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

View Construct and Data Evidence

UniProt name	AMPD2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 10–678； UniProt 211–879 Author chain B； PDBConstruct 10–678； UniProt 211–879 Author chain C； PDBConstruct 10–678； UniProt 211–879 Author chain D； PDBConstruct 10–678； UniProt 211–879

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	8hu6
Deposition date deposition_date	2022-12-22
Structure title title	AMP deaminase 2 in complex with AMP
Keywords keywords	Complex, Deaminase, AMP, IMP, Energy metabolism, HYDROLASE; HYDROLASE
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	41.27 Å
Radius of gyration Rg (electron density) rg_electron	40.43 Å
Forward intensity I(0) i0	1229200000.00
Molecular weight molecular_weight	289640.0 kDa
Excluded volume excluded_volume	362270 Å³
Envelope volume envelope_volume	453090 Å³
Hydration-shell volume shell_volume	87626 Å³
Envelope diameter envelope_diameter	135.5 Å
Shell Rg shell_rg	49.66 Å
Envelope Rg envelope_rg	40.31 Å
Shape Rg shape_rg	40.44 Å
Total Rg total_rg	40.81 Å
Total atoms total_atoms	40408
Residues n_residues	2483
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	126.8 Å
Rg (real space) rg_real	41.06 Å
Rg uncertainty (real space) rg_real_error	0.88 Å
I(0) (real space) i0_real	1.2290e+09
I(0) uncertainty (real space) i0_real_error	2.0360e+07
Rg (reciprocal space) rg_reciprocal	41.27 Å
I(0) (reciprocal space) i0_reciprocal	1229000000.0000
Solution quality estimate total_estimate	0.8848
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	53.4 Å
Skewness Skewness skewness	0.159
Kurtosis Kurtosis kurtosis	-0.402
Angular range angular_range	— – 0.1900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	458900000.0000
Real-space data points n_real_points	39
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.915; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.961; Smooth: 0.793

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	AMP deaminase 2
Molecular weight formula_weight	78752.6 kDa
EC 编号 ec_number	3.5.4.6
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	41188

MDYKDDDDKERDVLEREFQRVTISGEEKCGVPFTDLLDAAKSVVRALFIREKYMALSLQSFCPTTRRYLQQLAEKPLETRTYEQGPDTPVSADAPVHPPALEQHPYEHCEPSTMPGDLGLGLRMVRGVVHVYTRREPDEHCSEVELPYPDLQEFVADVNVLMALIINGPIKSFCYRRLQYLSSKFQMHVLLNEMKELAAQKKVPHRDFYNIRKVDTHIHASSCMNQKHLLRFIKRAMKRHLEEIVHVEQGREQTLREVFESMNLTAYDLSVDTLDVHADRNTFHRFDKFNAKYNPIGESVLREIFIKTDNRVSGKYFAHIIKEVMSDLEESKYQNAELRLSIYGRSRDEWDKLARWAVMHRVHSPNVRWLVQVPRLFDVYRTKGQLANFQEMLENIFLPLFEATVHPASHPELHLFLEHVDGFDSVDDESKPENHVFNLESPLPEAWVEEDNPPYAYYLYYTFANMAMLNHLRRQRGFHTFVLRPHCGEAGPIHHLVSAFMLAENISHGLLLRKAPVLQYLYYLAQIGIAMSPLSNNSLFLSYHRNPLPEYLSRGLMVSLSTDDPLQFHFTKEPLMEEYSIATQVWKLSSCDMCELARNSVLMSGFSHKVKSHWLGPNYTKEGPEGNDIRRTNVPDIRVGYRYETLCQELALITQAVQSEMLETIPEEAGITMSPGPQ

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	Spodoptera frugiperda

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	4

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	ADENOSINE MONOPHOSPHATE
Molecular weight formula_weight	347.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	780

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8. Citations (1)

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Unit-cell length a length_a	123.665 Å
Unit-cell length b length_b	163.563 Å
Unit-cell length c length_c	289.385 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	32

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	orthorhombic

Resolution resolution	2.330 Å
Low-resolution limit resolution_low	72.350 Å
R factor r_factor	0.2383
R_work r_work	0.2368
R_free r_free	0.2675

fit	/app/data/saxs_computation/hu/8hu6/8hu6.fit
pddf	/app/data/pr_computation/hu/8hu6/8hu6.pr.out
profile	/app/data/saxs_computation/hu/8hu6/8hu6.dat

AMP deaminase 2 in complex with AMP

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

AMP deaminase 2

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