6NTT | pdb_00006ntt

X-ray Crystal Structure of Soybean Trypsin Inhibitor (Kunitz) Complexed with 1,5-Disulfonyl Naphthalene

• PDB DOI: https://doi.org/10.2210/pdb6NTT/pdb

• Classification: PLANT PROTEIN
• Organism(s): Glycine max
• Expression System: Glycine max
• Mutation(s): No 


• Deposited: 2019-01-30 Released: 2019-03-20 
• Deposition Author(s): McPherson, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.306 (Depositor), 0.306 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

Lattice Interactions in Crystals of Soybean Trypsin Inhibitor (Kunitz) Produced by Inclusion of 1,5-Disulfonylnaphthalene

McPherson, A., Day, J., Larson, S.B.

(2019) Cryst Growth Des 19: 2963-2969

• DOI: https://doi.org/10.1021/acs.cgd.9b00164

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 49.51 kDa 
• Atom Count: 3,130 
• Modeled Residue Count: 351 
• Deposited Residue Count: 432 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Trypsin inhibitor A	A, B	216	Glycine max	Mutation(s): 0  Gene Names: KTI3
UniProt
Find proteins for P01070 (Glycine max) Explore P01070  Go to UniProtKB:  P01070

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
21D	C [auth A], E [auth B], F [auth B]	naphthalene-1,5-disulfonic acid C10 H8 O6 S2 XTEGVFVZDVNBPF-UHFFFAOYSA-N
MES	D [auth A], G [auth B], H [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.306 (Depositor), 0.306 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.88	α = 90
b = 64.68	β = 97.52
c = 69.08	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-03-20 
Deposition Author(s): McPherson, A.

Revision History  

• Version 1.0: 2019-03-20
  Type: Initial release
  
• Version 1.1: 2019-12-11
  Changes: Database references
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary