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1dss

STRUCTURE OF ACTIVE-SITE CARBOXYMETHYLATED D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM PALINURUS VERSICOLOR

Method: X-RAY DIFFRACTION Dmax: 92.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

D-GLYCERALDEHYDE-3-PHOSPHATE-DEHYDROGENASE

OrganismNot specified

UniProt P56649

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 G； UniProt 1–333 Chain R； UniProt 1–333 Fragment：NAD+ BINDING DOMAIN AND CATALYTIC DOMAIN Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 8 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.1；290 K；THE PROTEIN SOLUTIONS CONTAINED 0.5MM NAD+, 1.0MM EDTA, 1.6M AMMONIUM SULFATE IN 0.1M PHOSPHATE BUFFER(PH 6.1) AND AN ENZYME CONCENTRATION OF 8MG/ML; THE SOLUTION IN RESERVOIR CONTAINED 2.7M AMMONIUM SULFATE IN SAME BUFFER, ROOM TEMPERATURE OF 17 DEGREES C., temperature 290K Resolution 1.88 Å R-free 0.218

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 1DSS Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1CRW CRYSTAL STRUCTURE OF APO-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM PALINURUS VERSICOLOR AT 2.0A RESOLUTION Deposited 1999-08-16 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain G 1–333（333 aa）
Chain R 1–333（333 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.1；291 K；pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 18K
Resolution 2.00 Å R-free 0.226
1IHX Crystal structure of two D-glyceraldehyde-3-phosphate dehydrogenase complexes: a case of asymmetry Deposited 2001-04-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–333（333 aa）
Chain B 1–333（333 aa）
Chain C 1–333（333 aa）
Chain D 1–333（333 aa）
Not recorded SO4 SULFATE ION × 8 SND THIONICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.1；298 K；ammonium sulphate, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.80 Å R-free 0.204
1IHY GAPDH complexed with ADP-ribose Deposited 2001-04-20 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–333（333 aa）
Chain B 1–333（333 aa）
Chain C 1–333（333 aa）
Chain D 1–333（333 aa）
Not recorded SO4 SULFATE ION × 8 APR ADENOSINE-5-DIPHOSPHORIBOSE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；298 K；ammonium sulphate, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.00 Å R-free 0.207
1SZJ STRUCTURE OF HOLO-GLYCERALDEHYDE-3-PHOSPHATE-DEHYDROGENASE FROM PALINURUS VERSICOLOR REFINED 2.0 ANGSTROM RESOLUTION Deposited 1997-02-04 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain G 1–333（333 aa） Fragment：NAD+ BINDING DOMAIN AND CATALYTIC DOMAIN
Chain R 1–333（333 aa） Fragment：NAD+ BINDING DOMAIN AND CATALYTIC DOMAIN
Not recorded SO4 SULFATE ION × 8 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.1；280 K；THE PROTEIN SOLUTIONS CONTAINED 0.5MM NAD+, 1.0MM EDTA, 1.6M AMMONIUM SULPHATE IN 0.1M PHOSPHATE BUFFER (PH 6.1) AND AN ENZYME CONCENTRATION OF 8MG/ML; THE SOLUTION IN RESERVOIR CONTAINED 2.7M AMMONIUM SULPHATE IN SAME BUFFER. THE CRYSTALLIZATION WAS CARRIED OUT AT 280K.
Resolution 2.00 Å R-free 0.223

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

View Construct and Data Evidence
UniProt name G3P_PALVE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain G； PDBConstruct 1–333； UniProt 1–333 Author chain R； PDBConstruct 1–333； UniProt 1–333

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 1dss

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1dss
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1dss
Deposition date deposition_date1997-06-04
Structure title titleSTRUCTURE OF ACTIVE-SITE CARBOXYMETHYLATED D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM PALINURUS VERSICOLOR
Keywords keywords;ACTIVE-SITE CARBOXYMETHYLATION, D-GLYCERALDEHYDE-3-PHOSPHATE-DEHYDROGENASE, 'THE-HALF-OF-SITES' REACTION, MOLECULAR SYMMETRY ;; ACTIVE-SITE CARBOXYMETHYLATION
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier28.99 Å
Radius of gyration Rg (electron density) rg_electron28.74 Å
Forward intensity I(0) i088156400.00
Molecular weight molecular_weight73277.0 kDa
Excluded volume excluded_volume91505 ų
Envelope volume envelope_volume109340 ų
Hydration-shell volume shell_volume32120 ų
Envelope diameter envelope_diameter93.1 Å
Shell Rg shell_rg35.57 Å
Envelope Rg envelope_rg28.60 Å
Shape Rg shape_rg28.74 Å
Total Rg total_rg29.37 Å
Total atoms total_atoms5128
Residues n_residues664
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax92.7 Å
Rg (real space) rg_real29.00 Å
Rg uncertainty (real space) rg_real_error0.69 Å
I(0) (real space) i0_real8.8160e+07
I(0) uncertainty (real space) i0_real_error1.3830e+06
Rg (reciprocal space) rg_reciprocal29.00 Å
I(0) (reciprocal space) i0_reciprocal88160000.0000
Solution quality estimate total_estimate0.8976
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary28.6 Å
Skewness Skewness skewness0.303
Kurtosis Kurtosis kurtosis-0.586
Angular range angular_range— – 0.2750 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha28560000.0000
Real-space data points n_real_points56
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.928; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.945; Smooth: 0.936
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1dssg1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
Domain ID domain_idd1dssg2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.81 — FwdE/GAPDH domain-like
Superfamily Superfamily superfamilyd.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family Family familyd.81.1.1 — GAPDH-like
Domain ID domain_idd1dssr1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.3 — Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain
Domain ID domain_idd1dssr2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.81 — FwdE/GAPDH domain-like
Superfamily Superfamily superfamilyd.81.1 — Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain
Family Family familyd.81.1.1 — GAPDH-like

CATH v4.4 (4 domains)

Domain ID domain_id1dssG01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id1dssG02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily10 — Dihydrodipicolinate Reductase; domain 2
Domain ID domain_id1dssR01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id1dssR02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology360 — Dihydrodipicolinate Reductase; domain 2
Homologous superfamily homologous superfamily10 — Dihydrodipicolinate Reductase; domain 2
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8. Citations (3)

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9. Files and Curves (10)