6y4y

The crystal structure of human MACROD2 in space group P41212

Method: X-RAY DIFFRACTION Dmax: 93.6 Å Quality: EXCELLENT

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

Thioredoxin 1,ADP-ribose glycohydrolase MACROD2

Homo sapiens

UniProt A1Z1Q3

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 7–243 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.7;293 K;0.2 M Ammonium tartarate dibasic pH 6.7, 20% PEG 3350 Resolution 1.75 Å R-free 0.227
2 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 7–243 Not recorded TLA L(+)-TARTARIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.7;293 K;0.2 M Ammonium tartarate dibasic pH 6.7, 20% PEG 3350 Resolution 1.75 Å R-free 0.227
3 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 7–243 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.7;293 K;0.2 M Ammonium tartarate dibasic pH 6.7, 20% PEG 3350 Resolution 1.75 Å R-free 0.227
4 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain D; UniProt 7–243 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.7;293 K;0.2 M Ammonium tartarate dibasic pH 6.7, 20% PEG 3350 Resolution 1.75 Å R-free 0.227

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.

3 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MACD2_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 130–366; UniProt 7–243 Author chain B; PDBConstruct 130–366; UniProt 7–243 Author chain C; PDBConstruct 130–366; UniProt 7–243 Author chain D; PDBConstruct 130–366; UniProt 7–243

Thioredoxin 1,ADP-ribose glycohydrolase MACROD2

Homo sapiens

UniProt P0AA25

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 1–109 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.7;293 K;0.2 M Ammonium tartarate dibasic pH 6.7, 20% PEG 3350 Resolution 1.75 Å R-free 0.227
2 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 1–109 Not recorded TLA L(+)-TARTARIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.7;293 K;0.2 M Ammonium tartarate dibasic pH 6.7, 20% PEG 3350 Resolution 1.75 Å R-free 0.227
3 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 1–109 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.7;293 K;0.2 M Ammonium tartarate dibasic pH 6.7, 20% PEG 3350 Resolution 1.75 Å R-free 0.227
4 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain D; UniProt 1–109 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.7;293 K;0.2 M Ammonium tartarate dibasic pH 6.7, 20% PEG 3350 Resolution 1.75 Å R-free 0.227

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.

52 other PDB entries and 97 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name THIO_ECOLI
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 11–119; UniProt 1–109 Author chain B; PDBConstruct 11–119; UniProt 1–109 Author chain C; PDBConstruct 11–119; UniProt 1–109 Author chain D; PDBConstruct 11–119; UniProt 1–109

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.

SAXS scattering curve SAXS Profile

SAXS profile for 6y4y

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6y4y
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6y4y
Deposition date deposition_date2020-02-24
Structure title titleThe crystal structure of human MACROD2 in space group P41212
Keywords keywordsADP-ribosylhydrolase, macrodomain, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier30.94
Radius of gyration Rg (electron density) rg_electron30.25
Forward intensity I(0) i0146576000.00
Molecular weight molecular_weight97380.0 kDa
Excluded volume excluded_volume122620 ų
Envelope volume envelope_volume153290 ų
Hydration-shell volume shell_volume41618 ų
Envelope diameter envelope_diameter96.9
Shell Rg shell_rg38.02
Envelope Rg envelope_rg30.12
Shape Rg shape_rg30.24
Total Rg total_rg30.97
Total atoms total_atoms6840
Residues n_residues864
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

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

Maximum dimension Dmax dmax93.6
Rg (real space) rg_real30.75
Rg uncertainty (real space) rg_real_error0.51
I(0) (real space) i0_real1.4660e+08
I(0) uncertainty (real space) i0_real_error2.0100e+06
Rg (reciprocal space) rg_reciprocal30.83
I(0) (reciprocal space) i0_reciprocal146600000.0000
Solution quality estimate total_estimate0.9105
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary42.2
Skewness Skewness skewness0.074
Kurtosis Kurtosis kurtosis-0.633
Angular range angular_range— – 0.2550 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha43630000.0000
Real-space data points n_real_points52
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.962; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.952

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

8. Citations (1)

9. Files and Curves (10)