1tk2

Crystal Structure of the Complex formed between Alkaline Proteinase Savinase and Gramicidin S at 1.5A Resolution

Method: X-RAY DIFFRACTION Dmax: 52.5 Å Quality: EXCELLENT

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

SUBTILISIN SAVINASE

OrganismNot specified

UniProt P29600

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–269 Not recorded GRAMICIDIN S × 1 CA CALCIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.5;0.33M NACL, 10% PEG 4000, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K Resolution 1.54 Å R-free 0.189

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.

20 other PDB entries and 22 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SUBS_BACLE
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–263; 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 1tk2

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1tk2
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1tk2
Deposition date deposition_date2004-06-08
Structure title titleCrystal Structure of the Complex formed between Alkaline Proteinase Savinase and Gramicidin S at 1.5A Resolution
Keywords keywordsGRAMICIDIN, ANTIBIOTIC, ANTIFUNGAL, ANTIBACTERIAL, CYCLIC GRAMICIDIN, MEMBRANE ION CHANNEL, HYDROLASE-ANTIBIOTIC COMPLEX; HYDROLASE/ANTIBIOTIC
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier17.65
Radius of gyration Rg (electron density) rg_electron16.45
Forward intensity I(0) i014717500.00
Molecular weight molecular_weight27911.0 kDa
Excluded volume excluded_volume34497 ų
Envelope volume envelope_volume37221 ų
Hydration-shell volume shell_volume18360 ų
Envelope diameter envelope_diameter52.5
Shell Rg shell_rg23.18
Envelope Rg envelope_rg16.61
Shape Rg shape_rg16.46
Total Rg total_rg17.37
Total atoms total_atoms1963
Residues n_residues275
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 dmax52.5
Rg (real space) rg_real17.47
Rg uncertainty (real space) rg_real_error0.21
I(0) (real space) i0_real1.4720e+07
I(0) uncertainty (real space) i0_real_error1.5350e+05
Rg (reciprocal space) rg_reciprocal17.49
I(0) (reciprocal space) i0_reciprocal14720000.0000
Solution quality estimate total_estimate0.9005
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.1
Skewness Skewness skewness-0.012
Kurtosis Kurtosis kurtosis-0.538
Angular range angular_range— – 0.4500 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha4531000.0000
Real-space data points n_real_points76
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.912; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.997

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1tk2a_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.41 — Subtilisin-like
Superfamily Superfamily superfamilyc.41.1 — Subtilisin-like
Family Family familyc.41.1.1 — Subtilases
Domain ID domain_idd1tk2b_
Class classj — Peptides
Fold Fold foldj.1 — Membrane ion channel-forming peptide antibiotics containing D-aminoacids
Superfamily Superfamily superfamilyj.1.1 — Membrane ion channel-forming peptide antibiotics containing D-aminoacids
Family Family familyj.1.1.1 — Gramicidin

CATH v4.4 (1 domains)

Domain ID domain_id1tk2A00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily200 — Peptidase S8/S53 domain

8. Citations (1)

9. Files and Curves (10)