← Back to search
1dvr

STRUCTURE OF A MUTANT ADENYLATE KINASE LIGATED WITH AN ATP-ANALOGUE SHOWING DOMAIN CLOSURE OVER ATP

Method: X-RAY DIFFRACTION Dmax: 82.7 Å Quality: GOOD
▼

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

ADENYLATE KINASE

Saccharomyces cerevisiae

UniProt P07170

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 3–221 Chain B； UniProt 3–221 Mutation：D89V, R165I ATF PHOSPHODIFLUOROMETHYLPHOSPHONIC ACID-ADENYLATE ESTER × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.36 Å

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 1DVR Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AKY HIGH-RESOLUTION STRUCTURES OF ADENYLATE KINASE FROM YEAST LIGATED WITH INHIBITOR AP5A, SHOWING THE PATHWAY OF PHOSPHORYL TRANSFER Deposited 1995-07-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 3–221（219 aa）
Not recorded AP5 BIS(ADENOSINE)-5'-PENTAPHOSPHATE × 1 IMD IMIDAZOLE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.63 Å
2AKY HIGH-RESOLUTION STRUCTURES OF ADENYLATE KINASE FROM YEAST LIGATED WITH INHIBITOR AP5A, SHOWING THE PATHWAY OF PHOSPHORYL TRANSFER Deposited 1995-07-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 3–221（219 aa）
Not recorded MG MAGNESIUM ION × 1 AP5 BIS(ADENOSINE)-5'-PENTAPHOSPHATE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.96 Å
3AKY STABILITY, ACTIVITY AND STRUCTURE OF ADENYLATE KINASE MUTANTS Deposited 1995-07-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 3–221（219 aa）
Mutation：I213F AP5 BIS(ADENOSINE)-5'-PENTAPHOSPHATE × 1 IMD IMIDAZOLE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.23 Å

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

View Construct and Data Evidence
UniProt name KAD1_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–219； UniProt 3–221 Author chain B； PDBConstruct 1–219； UniProt 3–221

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 1dvr

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1dvr
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id1dvr
Deposition date deposition_date1995-12-14
Structure title titleSTRUCTURE OF A MUTANT ADENYLATE KINASE LIGATED WITH AN ATP-ANALOGUE SHOWING DOMAIN CLOSURE OVER ATP
Keywords keywordsNUCLEOSIDE MONOPHOSPHATE KINASE, MYOKINASE, TRANSFERASE (PHOSPHOTRANSFERASE); TRANSFERASE (PHOSPHOTRANSFERASE)
Experimental Method methodX-RAY DIFFRACTION
▼

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

Radius of gyration Rg (Guinier) rg_guinier24.91 Å
Radius of gyration Rg (electron density) rg_electron24.16 Å
Forward intensity I(0) i042217200.00
Molecular weight molecular_weight49032.0 kDa
Excluded volume excluded_volume60986 ų
Envelope volume envelope_volume74522 ų
Hydration-shell volume shell_volume26021 ų
Envelope diameter envelope_diameter81.2 Å
Shell Rg shell_rg30.84 Å
Envelope Rg envelope_rg23.97 Å
Shape Rg shape_rg24.21 Å
Total Rg total_rg24.77 Å
Total atoms total_atoms3432
Residues n_residues440
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
▼

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

Maximum dimension Dmax dmax82.7 Å
Rg (real space) rg_real24.86 Å
Rg uncertainty (real space) rg_real_error0.56 Å
I(0) (real space) i0_real4.2220e+07
I(0) uncertainty (real space) i0_real_error5.9120e+05
Rg (reciprocal space) rg_reciprocal24.87 Å
I(0) (reciprocal space) i0_reciprocal42220000.0000
Solution quality estimate total_estimate0.8134
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary28.9 Å
Skewness Skewness skewness0.276
Kurtosis Kurtosis kurtosis-0.513
Angular range angular_range— – 0.3200 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7605000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.867; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.000
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

▼

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1dvra1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.1 — Nucleotide and nucleoside kinases
Domain ID domain_idd1dvra2
Class classg — Small proteins
Fold Fold foldg.41 — Rubredoxin-like
Superfamily Superfamily superfamilyg.41.2 — Microbial and mitochondrial ADK, insert 'zinc finger' domain
Family Family familyg.41.2.1 — Microbial and mitochondrial ADK, insert 'zinc finger' domain
Domain ID domain_idd1dvrb1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.1 — Nucleotide and nucleoside kinases
Domain ID domain_idd1dvrb2
Class classg — Small proteins
Fold Fold foldg.41 — Rubredoxin-like
Superfamily Superfamily superfamilyg.41.2 — Microbial and mitochondrial ADK, insert 'zinc finger' domain
Family Family familyg.41.2.1 — Microbial and mitochondrial ADK, insert 'zinc finger' domain

CATH v4.4 (2 domains)

Domain ID domain_id1dvrA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id1dvrB00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
▶

8. Citations (7)

▶

9. Files and Curves (10)