6NTT: Soybean Trypsin Inhibitor

X-ray Crystal Structure of Soybean Trypsin Inhibitor (Kunitz) Complexed with 1,5-Disulfonyl Naphthalene. Determined by X-ray diffraction at 2.4 Å resolution. Released 20 Mar 2019.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Glycine max
Chains: 2
Atoms: 3,130
Mol. weight: 49.51 kDa
Ligands: 21D
Released: 20 Mar 2019

Explore 6NTT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6NTT contains 14 α-helices and 45 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	1
α-helix	3	1
β-strand	4	1	2
α-helix	9	1
β-strand	10	1	2
α-helix	11	1
β-strand	12	1	3
β-strand	15-21	7	4
β-strand	29-32	4	5
β-strand	42-45	4	5
β-strand	53	1	5
β-strand	55-59	5	4
β-strand	66	1	3
α-helix	67	1
β-strand	68	1	1
β-strand	73-77	5	4
α-helix	78-79	2
β-strand	82	1	6
α-helix	84-86	3
β-strand	92	1	4
β-strand	94-96	3	5
β-strand	104-106	3	5
β-strand	113	1	5
α-helix	114	1
β-strand	116-122	7	4
β-strand	131-137	7	4
β-strand	146-147	2	4
β-strand	148-153	6	5
β-strand	158-163	6	5
α-helix	168-169	2
β-strand	170-175	6	4

Chain B: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	7
α-helix	3	1
β-strand	4	1	8
α-helix	9	1
β-strand	10	1	8
α-helix	11	1
β-strand	12	1	9
β-strand	15-21	7	10
β-strand	29-32	4	11
β-strand	42-45	4	11
β-strand	56-59	4	10
β-strand	66	1	9
β-strand	68	1	7
β-strand	73-77	5	10
α-helix	78-79	2
β-strand	82	1	6
α-helix	84-86	3
β-strand	92	1	10
β-strand	94-96	3	11
β-strand	104-106	3	11
β-strand	113	1	11
α-helix	114	1
β-strand	116-122	7	10
β-strand	131-137	7	10
β-strand	146-147	2	10
β-strand	148-152	5	11
β-strand	159-163	5	11
β-strand	170-175	6	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Trypsin inhibitor A	A, B	protein	216	Glycine max	P01070 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6NTT_1 Trypsin inhibitor A (chains A, B)
MKSTIFFLFLFCAFTTSYLPSAIADFVLDNEGNPLENGGTYYILSDITAFGGIRAAPTGN
ERCPLTVVQSRNELDKGIGTIISSPYRIRFIAEGHPLSLKFDSFAVIMLCVGIPTEWSVV
EDLPEGPAVKIGENKDAMDGWFRLERVSDDEFNNYKLVFCPQQAEDDKCGDIGISIDHDD
GTRRLVVSKNKPLVVQFQKLDKESLAKKNHGLSRSE

Ligands and cofactors

ID	Name	Formula	Copies
21D	naphthalene-1,5-disulfonic acid	C10 H8 O6 S2	3

Water and common crystallization additives (MES) are not listed.

Primary citation

Lattice Interactions in Crystals of Soybean Trypsin Inhibitor (Kunitz) Produced by Inclusion of 1,5-Disulfonylnaphthalene. McPherson, A., Day, J., Larson, S.B. Cryst Growth Des (2019) 19:2963-2969. DOI 10.1021/acs.cgd.9b00164

Other PDB entries of the same protein (UniProt P01070 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1AVW 1.75 Å, Complex porcine pancreatic trypsin/soybean trypsin inhibitor, orthorhombic crystal form
1AVX 1.9 Å, Complex porcine pancreatic trypsin/soybean trypsin inhibitor, tetragonal crystal form
6O1F 2.15 Å, Complex between soybean trypsin inhibitor beta1-tryptase and a humanized fab
1AVU 2.3 Å, Trypsin inhibitor from soybean (STI)
1BA7 2.5 Å, Soybean trypsin inhibitor

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