6r9w

Crystal structure of InhA in complex with AP-124 inhibitor

Method: X-RAY DIFFRACTION Dmax: 125.2 Å Quality: EXCELLENT

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

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

Mycobacterium tuberculosis H37Rv

UniProt P9WGR1

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 JVZ (2~{S})-1-(benzimidazol-1-yl)-3-(2,3-dihydro-1~{H}-inden-5-yloxy)propan-2-ol × 2 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;292.15 K;17% w/v PEG 4000, 0.1 M ADA pH 6.8, 6 mM DMSO, 0.1 M ammonium acetate, 1% glycerol, 4.5 mM NAD Resolution 1.75 Å R-free 0.227
2 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain C; UniProt 1–269 Chain D; UniProt 1–269 Chain E; UniProt 1–269 Chain F; UniProt 1–269 Not recorded NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;292.15 K;17% w/v PEG 4000, 0.1 M ADA pH 6.8, 6 mM DMSO, 0.1 M ammonium acetate, 1% glycerol, 4.5 mM NAD 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 69 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 4–272; UniProt 1–269 Author chain B; PDBConstruct 4–272; UniProt 1–269 Author chain C; PDBConstruct 4–272; UniProt 1–269 Author chain D; PDBConstruct 4–272; UniProt 1–269 Author chain E; PDBConstruct 4–272; UniProt 1–269 Author chain F; PDBConstruct 4–272; 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 6r9w

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6r9w
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6r9w
Deposition date deposition_date2019-04-04
Structure title titleCrystal structure of InhA in complex with AP-124 inhibitor
Keywords keywordsInhibitor, complex, OXIDOREDUCTASE, antibiotic resistance; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier39.38
Radius of gyration Rg (electron density) rg_electron38.77
Forward intensity I(0) i0441765000.00
Molecular weight molecular_weight170940.0 kDa
Excluded volume excluded_volume213790 ų
Envelope volume envelope_volume281040 ų
Hydration-shell volume shell_volume59043 ų
Envelope diameter envelope_diameter131.3
Shell Rg shell_rg45.91
Envelope Rg envelope_rg38.19
Shape Rg shape_rg38.78
Total Rg total_rg39.11
Total atoms total_atoms24006
Residues n_residues1571
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 dmax125.2
Rg (real space) rg_real39.19
Rg uncertainty (real space) rg_real_error1.26
I(0) (real space) i0_real4.4180e+08
I(0) uncertainty (real space) i0_real_error7.9700e+06
Rg (reciprocal space) rg_reciprocal39.31
I(0) (reciprocal space) i0_reciprocal441800000.0000
Solution quality estimate total_estimate0.9025
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary53.2
Skewness Skewness skewness0.130
Kurtosis Kurtosis kurtosis-0.581
Angular range angular_range— – 0.2000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha102400000.0000
Real-space data points n_real_points41
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.933; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.931

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd6r9wa_
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.2.1.2 — Tyrosine-dependent oxidoreductases
Domain ID domain_idd6r9wb_
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.2.1.2 — Tyrosine-dependent oxidoreductases
Domain ID domain_idd6r9wc_
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.2.1.2 — Tyrosine-dependent oxidoreductases
Domain ID domain_idd6r9wd_
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.2.1.2 — Tyrosine-dependent oxidoreductases
Domain ID domain_idd6r9we_
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.2.1.2 — Tyrosine-dependent oxidoreductases
Domain ID domain_idd6r9wf_
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.2.1.2 — Tyrosine-dependent oxidoreductases

CATH v4.4 (6 domains)

Domain ID domain_id6r9wA00
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_id6r9wB00
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_id6r9wC00
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_id6r9wD00
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_id6r9wE00
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_id6r9wF00
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)