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4lc0

Identifying ligand binding hot spots in proteins using brominated fragments

Method: X-RAY DIFFRACTION Dmax: 76.8 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Elongation factor Tu-A

Thermus thermophilus

UniProt P60338

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 3–406 Not recorded GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 NH4 AMMONIUM ION × 1 SO4 SULFATE ION × 7 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.6；292 K；1.8M ammonium sulfate, 15% sucrose, 0.1M Tris-HCl, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 292K Resolution 2.22 Å R-free 0.201
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 3–406 Not recorded GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 MG MAGNESIUM ION × 2 NH4 AMMONIUM ION × 2 SO4 SULFATE ION × 14 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.6；292 K；1.8M ammonium sulfate, 15% sucrose, 0.1M Tris-HCl, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 292K Resolution 2.22 Å R-free 0.201

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 4LC0 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AIP EF-TU EF-TS COMPLEX FROM THERMUS THERMOPHILUS Deposited 1997-04-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–405（405 aa）
Chain B 1–405（405 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；60 MM CACODYLATE, PH 6.5 70 MM AMMONIUM SULFATE 8% PEG 8000
Resolution 3.00 Å R-free 0.289
1AIP EF-TU EF-TS COMPLEX FROM THERMUS THERMOPHILUS Deposited 1997-04-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 1–405（405 aa）
Chain F 1–405（405 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；60 MM CACODYLATE, PH 6.5 70 MM AMMONIUM SULFATE 8% PEG 8000
Resolution 3.00 Å R-free 0.289
1EXM CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS ELONGATION FACTOR TU (EF-TU) IN COMPLEX WITH THE GTP ANALOGUE GPPNHP. Deposited 2000-05-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–406（405 aa） Fragment：INTACT WILD-TYPE EF-TU
Not recorded MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；20mM Sodium cacodylate, 5mM Magnesium sulfate, 38-44% Ammonium sulfate, 7-10 mg/mL EF-Tu, molar ratio EF-Tu:GppNHp = 1:5, pH 7.0, VAPOR DIFFUSION, HANGING DROP
Resolution 1.70 Å R-free 0.243
4H9G Probing EF-Tu with a very small brominated fragment library identifies the CCA pocket Deposited 2012-09-24 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–406（405 aa）
Not recorded GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 NH4 AMMONIUM ION × 1 SO4 SULFATE ION × 8 14J 5-bromofuran-2-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；292 K；1.8M ammonium sulfate, 15% sucrose, 0.1M tris, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 1.93 Å R-free 0.184
4LBV Identifying ligand binding hot spots in proteins using brominated fragments Deposited 2013-06-21 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 3–406（404 aa）
Not recorded GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 NH4 AMMONIUM ION × 1 CL CHLORIDE ION × 1 SO4 SULFATE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；292 K；1.8M ammonium sulfate, 15% sucrose, 0.1M Tris-HCl, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 2.03 Å R-free 0.193
4LBV Identifying ligand binding hot spots in proteins using brominated fragments Deposited 2013-06-21 Different ligand/ion Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 3–406（404 aa）
Not recorded GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 MG MAGNESIUM ION × 2 NH4 AMMONIUM ION × 2 CL CHLORIDE ION × 2 SO4 SULFATE ION × 16 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；292 K；1.8M ammonium sulfate, 15% sucrose, 0.1M Tris-HCl, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 2.03 Å R-free 0.193
4LBW Identifying ligand binding hot spots in proteins using brominated fragments Deposited 2013-06-21 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 3–406（404 aa）
Not recorded GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 NH4 AMMONIUM ION × 1 SO4 SULFATE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；292 K；1.8M ammonium sulfate, 15% sucrose, 0.1M Tris-HCl, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 1.74 Å R-free 0.194
4LBW Identifying ligand binding hot spots in proteins using brominated fragments Deposited 2013-06-21 Different ligand/ion Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 3–406（404 aa）
Not recorded GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 MG MAGNESIUM ION × 2 NH4 AMMONIUM ION × 2 SO4 SULFATE ION × 16 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；292 K；1.8M ammonium sulfate, 15% sucrose, 0.1M Tris-HCl, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 1.74 Å R-free 0.194
4LBY Identifying ligand binding hot spots in proteins using brominated fragments Deposited 2013-06-21 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 3–406（404 aa）
Not recorded GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 NH4 AMMONIUM ION × 1 SO4 SULFATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；292 K；1.8M ammonium sulfate, 15% sucrose, 0.1M Tris-HCl, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 2.69 Å R-free 0.207
4LBZ Identifying ligand binding hot spots in proteins using brominated fragments Deposited 2013-06-21 Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 3–406（404 aa）
Not recorded GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 NH4 AMMONIUM ION × 1 SO4 SULFATE ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；292 K；1.8M ammonium sulfate, 15% sucrose, 0.1M Tris-HCl, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 2.22 Å R-free 0.212
4LBZ Identifying ligand binding hot spots in proteins using brominated fragments Deposited 2013-06-21 Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 3–406（404 aa）
Not recorded GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 MG MAGNESIUM ION × 2 NH4 AMMONIUM ION × 2 SO4 SULFATE ION × 14 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；292 K；1.8M ammonium sulfate, 15% sucrose, 0.1M Tris-HCl, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Resolution 2.22 Å R-free 0.212

7 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name EFTU1_THETH
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–404； UniProt 3–406

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 4lc0

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4lc0
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4lc0
Deposition date deposition_date2013-06-21
Structure title titleIdentifying ligand binding hot spots in proteins using brominated fragments
Keywords keywordsGTPase, PROTEIN BINDING; PROTEIN BINDING
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_guinier22.35 Å
Radius of gyration Rg (electron density) rg_electron21.45 Å
Forward intensity I(0) i036533300.00
Molecular weight molecular_weight45228.0 kDa
Excluded volume excluded_volume56018 ų
Envelope volume envelope_volume64916 ų
Hydration-shell volume shell_volume24882 ų
Envelope diameter envelope_diameter75.8 Å
Shell Rg shell_rg28.59 Å
Envelope Rg envelope_rg21.69 Å
Shape Rg shape_rg21.43 Å
Total Rg total_rg22.36 Å
Total atoms total_atoms3167
Residues n_residues403
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 dmax76.8 Å
Rg (real space) rg_real22.27 Å
Rg uncertainty (real space) rg_real_error0.52 Å
I(0) (real space) i0_real3.6530e+07
I(0) uncertainty (real space) i0_real_error4.9700e+05
Rg (reciprocal space) rg_reciprocal22.29 Å
I(0) (reciprocal space) i0_reciprocal36530000.0000
Solution quality estimate total_estimate0.6401
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.8 Å
Skewness Skewness skewness0.246
Kurtosis Kurtosis kurtosis-0.365
Angular range angular_range— – 0.3550 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8704000.0000
Real-space data points n_real_points67
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.778; Stabil: 1.000; Sysdev: 0.328; Positv: 1.000; Valcen: 0.999; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd4lc0a1
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.37.1.8 — G proteins
Domain ID domain_idd4lc0a2
Class classb — All beta proteins
Fold Fold foldb.43 — Reductase/isomerase/elongation factor common domain
Superfamily Superfamily superfamilyb.43.3 — Translation proteins
Family Family familyb.43.3.0 — automated matches
Domain ID domain_idd4lc0a3
Class classb — All beta proteins
Fold Fold foldb.44 — Elongation factor/aminomethyltransferase common domain
Superfamily Superfamily superfamilyb.44.1 — EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain
Family Family familyb.44.1.0 — automated matches

CATH v4.4 (3 domains)

Domain ID domain_id4lc0A01
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_id4lc0A02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily10 — Translation factors
Domain ID domain_id4lc0A03
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily10 — Translation factors
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8. Citations (1)

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9. Files and Curves (10)