6SY3: Cationic Trypsin

Cationic Trypsin in Complex with a D-DiPhe-Pro-pyridine derivative. Determined by X-ray diffraction at 0.95 Å resolution. Released 13 May 2020.

Method: X-ray diffraction
Resolution: 0.95 Å
Organism: Bos taurus
Chains: 1
Atoms: 2,055
Mol. weight: 26.35 kDa
Ligands: LXW, CA
Released: 13 May 2020

Explore 6SY3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6SY3 contains 7 α-helices and 20 β-strands across 1 chain. 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: 7 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	1
β-strand	20-21	2	2
β-strand	30-34	5	3
β-strand	40-48	9	3
β-strand	51-54	4	3
α-helix	56-58	3
β-strand	64-67	4	3
β-strand	81-90	10	3
β-strand	104-108	5	3
β-strand	115	1	4
β-strand	118	1	4
β-strand	122	1	2
α-helix	123-124	2
α-helix	128-130	3
β-strand	135-140	6	2
β-strand	156-162	7	2
α-helix	163-164	2
α-helix	165-171	7
β-strand	180-183	4	2
β-strand	189	1	1
β-strand	198-201	4	2
β-strand	204-215	8	2
β-strand	221A	1	5
β-strand	224	1	5
β-strand	226-230	5	2
α-helix	231-234	4
α-helix	235-242	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cationic Trypsin	A	protein	246	Bos taurus	P00760 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6SY3_1 Cationic Trypsin (chains A)
MKTFIFLALLGAAVAFPVDDDDKIVGGYTCGANTVPYQVSLNSGYHFCGGSLINSQWVVS
AAHCYKSGIQVRLGEDNINVVEGNEQFISASKSIVHPSYNSNTLNNDIMLIKLKSAASLN
SRVASISLPTSCASAGTQCLISGWGNTKSSGTSYPDVLKCLKAPILSDSSCKSAYPGQIT
SNMFCAGYLEGGKDSCQGDSGGPVVCSGKLQGIVSWGSGCAQKNKPGVYTKVCNYVSWIK
QTIASN

Ligands and cofactors

ID	Name	Formula	Copies
LXW	(2~{S})-1-[(2~{R})-2-azanyl-3,3-diphenyl-propanoyl]-~{N}-(pyridin-4-ylmethyl)py…	C26 H28 N4 O2	1
CA	Calcium ion	Ca	1

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

Primary citation

Protein-Induced Change in Ligand Protonation during Trypsin and Thrombin Binding: Hint on Differences in Selectivity Determinants of Both Proteins? Ngo, K., Collins-Kautz, C., Gerstenecker, S. et al. J Med Chem (2020) 63:3274-3289. DOI 10.1021/acs.jmedchem.9b02061 · PubMed

Other PDB entries of the same protein (UniProt P00760 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4I8H 0.75 Å, Bovine trypsin at 0.75 resolution
5MN1 0.79 Å, Cationic trypsin in complex with 2-aminopyridine (deuterated sample at 100 K)
5MNK 0.8 Å, Cationic trypsin in complex with benzylamine (deuterated sample at 100 K)
3MFJ 0.8 Å, Bovine trypsin at 0.8 A resolution, restrained refinement
3MI4 0.8 Å, Bovine trypsin at 0.8 A resolution, non-restrained refinement
4I8G 0.8 Å, Bovine trypsin at 0.8 resolution
4I8K 0.85 Å, Bovine trypsin at 0.85 resolution
5MNN 0.86 Å, Cationic trypsin in complex with N-amidinopiperidine (deuterated sample at 100 K)
5MNG 0.86 Å, Cationic trypsin in complex with benzamidine (deuterated sample at 100 K)
4I8J 0.87 Å, Bovine trypsin at 0.87 A resolution
4I8L 0.87 Å, Bovine trypsin at 0.87 resolution
4XOJ 0.91 Å, Structure of bovine trypsin in complex with analogues of sunflower inhibitor 1 (SFTI-1)

Browse structure collections

About this viewer

MolViewer shows 6SY3 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.