4Y11: Trypsin

Trypsin in complex with with BPTI mutant (2S)-2-amino-4,4,4-trifluorobutanoic acid. Determined by X-ray diffraction at 1.3 Å resolution. Released 24 Jun 2015.

Method: X-ray diffraction
Resolution: 1.3 Å
Organism: Bos taurus
Chains: 2
Atoms: 2,605
Mol. weight: 30.95 kDa
Ligands: CA
Released: 24 Jun 2015

Explore 4Y11 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4Y11 contains 10 α-helices and 22 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 E: 7 helices, 18 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
α-helix	111-114	4
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	165-171	7
β-strand	180-183	4	2
β-strand	191	1	1
β-strand	200-203	4	2
β-strand	206-213	8	2
β-strand	224-228	5	2
α-helix	229-232	4
α-helix	233-241	9

Chain I: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3
α-helix	8-9	2
β-strand	14	1	2
β-strand	18-24	7	5
β-strand	29-35	7	5
β-strand	45	1	5
α-helix	48-55	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cationic trypsin	E	protein	223	Bos taurus	P00760 (AlphaFold model)
Pancreatic trypsin inhibitor	I	protein	58	Bos taurus	P00974 (AlphaFold model)

Sequence of entity 1 (E), FASTA

>4Y11_1 Cationic trypsin (chains E)
IVGGYTCGANTVPYQVSLNSGYHFCGGSLINSQWVVSAAHCYKSGIQVRLGEDNINVVEG
NEQFISASKSIVHPSYNSNTLNNDIMLIKLKSAASLNSRVASISLPTSCASAGTQCLISG
WGNTKSSGTSYPDVLKCLKAPILSDSSCKSAYPGQITSNMFCAGYLEGGKDSCQGDSGGP
VVCSGKLQGIVSWGSGCAQKNKPGVYTKVCNYVSWIKQTIASN

Sequence of entity 2 (I), FASTA

>4Y11_2 Pancreatic trypsin inhibitor (chains I)
RPDFCLEPPYTGPCXARIIRYFYNAKAGLCQTFVYGGCRAKRNNFKSAEDCMRTCGGA

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1

Water and common crystallization additives (SO4, GOL) are not listed.

Primary citation

Fluorine teams up with water to restore inhibitor activity to mutant BPTI. Ye, S., Loll, B., Berger, A.A. et al. Chem Sci (2015) 6:5246-5254. DOI 10.1039/c4sc03227f · 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

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