4oxn

Substrate-like binding mode of inhibitor PT155 to the Mycobacterium tuberculosis enoyl-ACP reductase InhA

Method: X-RAY DIFFRACTION Dmax: 78.8 Å Quality: GOOD

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

Enoyl-[acyl-carrier-protein] reductase [NADH]

Mycobacterium tuberculosis

UniProt P0A5Y6

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 1–269 Chain B; UniProt 1–269 Not recorded NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 1S5 5-(4-amino-2-methylphenoxy)-2-hexyl-4-hydroxy-1-methylpyridinium × 4 CL CHLORIDE ION × 4 2NV 3,6,9,12,15-pentaoxaoctadecan-17-amine × 16 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8;298 K;100 mM HEPES pH 8.0, 32% Jeffamine ED-2001 pH 7.0 Resolution 2.29 Å R-free 0.205

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.

43 other PDB entries and 56 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name INHA_MYCTU
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 21–289; UniProt 1–269 Author chain B; PDBConstruct 21–289; UniProt 1–269

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 4oxn

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id4oxn
Deposition date deposition_date2014-02-05
Structure title titleSubstrate-like binding mode of inhibitor PT155 to the Mycobacterium tuberculosis enoyl-ACP reductase InhA
Keywords keywords;Bacterial fatty acid biosynthesis, conformational profile of enzyme-inhibitor complex, inhibition kinetics, substrate-binding loop refolding, OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex ;; OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier24.80
Radius of gyration Rg (electron density) rg_electron23.93
Forward intensity I(0) i055659800.00
Molecular weight molecular_weight58564.0 kDa
Excluded volume excluded_volume73608 ų
Envelope volume envelope_volume84993 ų
Hydration-shell volume shell_volume29093 ų
Envelope diameter envelope_diameter81.3
Shell Rg shell_rg31.72
Envelope Rg envelope_rg24.29
Shape Rg shape_rg23.93
Total Rg total_rg24.82
Total atoms total_atoms4109
Residues n_residues529
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 dmax78.8
Rg (real space) rg_real24.74
Rg uncertainty (real space) rg_real_error0.58
I(0) (real space) i0_real5.5660e+07
I(0) uncertainty (real space) i0_real_error7.9460e+05
Rg (reciprocal space) rg_reciprocal24.75
I(0) (reciprocal space) i0_reciprocal55660000.0000
Solution quality estimate total_estimate0.8985
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.8
Skewness Skewness skewness0.308
Kurtosis Kurtosis kurtosis-0.398
Angular range angular_range— – 0.3200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha10400000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.902; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.973

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id4oxnA00
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_id4oxnB00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain

8. Citations (1)

9. Files and Curves (10)