4NIY: Cationic trypsin

Crystal structure of trypsiligase (K60E/N143H/Y151H/D189K trypsin) complexed to YRH-ecotin (M84Y/M85R/A86H ecotin). Determined by X-ray diffraction at 2.84 Å resolution. Released 19 Feb 2014.

Method: X-ray diffraction
Resolution: 2.84 Å
Organisms: Bos taurus, Escherichia coli
Chains: 8
Atoms: 10,574
Mol. weight: 158.56 kDa
Ligands: CA, ZN
Released: 19 Feb 2014

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

Secondary structure: helices and β-sheets

4NIY contains 54 α-helices and 138 β-strands across 8 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.

Chains A and C: 8 helices, 22 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	72	1	4
β-strand	81-90	10	3
β-strand	95	1	5
β-strand	100	1	5
β-strand	104-108	5	3
β-strand	122	1	2
α-helix	123-124	2
α-helix	128-130	3
β-strand	135-140	6	2
β-strand	154	1	4
α-helix	155	1
β-strand	156-161	6	2
β-strand	162	1	6
α-helix	163-164	2
α-helix	165-171	7
β-strand	180-183	4	6
β-strand	189	1	1
β-strand	198-201	4	2
β-strand	204-212	5	2
β-strand	213-217	5	6
β-strand	226-229	4	6
α-helix	231-234	4
α-helix	235-243	9

Chain B: 7 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	20-21	2	7
β-strand	30-34	5	8
β-strand	40-48	9	8
β-strand	51-54	4	8
α-helix	56-58	3
β-strand	64-67	4	8
β-strand	72	1	9
β-strand	81-90	10	8
β-strand	95	1	10
β-strand	100	1	10
β-strand	104-108	5	8
β-strand	122	1	7
α-helix	123-124	2
α-helix	128-130	3
β-strand	135-140	6	7
β-strand	154	1	9
β-strand	156-162	7	7
α-helix	163-164	2
α-helix	165-171	7
β-strand	180-183	4	7
β-strand	198-201	4	7
β-strand	204-217	10	7
β-strand	226-230	5	7
α-helix	231-234	4
α-helix	235-243	9

Chain D: 7 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	21	1	17
β-strand	30-34	5	18
β-strand	40-48	9	18
β-strand	51-54	4	18
α-helix	56-58	3
β-strand	64-67	4	18
β-strand	72	1	19
β-strand	81-90	10	18
β-strand	95	1	20
β-strand	100	1	20
β-strand	104-108	5	18
β-strand	122	1	17
α-helix	123-124	2
α-helix	128-130	3
β-strand	135-140	6	17
β-strand	154	1	19
β-strand	156-161	6	17
β-strand	162	1	21
α-helix	163-164	2
α-helix	165-171	7
β-strand	180-183	4	21
β-strand	198-201	4	17
β-strand	204-212	5	17
β-strand	213-216	4	21
β-strand	226-229	4	21
α-helix	231-233	3
α-helix	235-243	9

Chain E: 7 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
α-helix	13-16	4
β-strand	20-25	6	22
α-helix	27-29	3
α-helix	33-35	3
β-strand	36-48	13	23
β-strand	53-54	2	6
β-strand	55	1	24
β-strand	58-64	7	22
β-strand	69-75	7	22
α-helix	78-80	3
β-strand	81-83	3	6
α-helix	85-87	3
β-strand	93-98	6	23
β-strand	99	1	24
α-helix	102-105	4
β-strand	106-108	3	23
β-strand	115-120	6	22
β-strand	124-132	9	23
β-strand	137-138	2	23
β-strand	140-141	2	25

Chain F: 6 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
α-helix	13-16	4
β-strand	20-25	6	25
α-helix	27-29	3
α-helix	33-35	3
β-strand	36-48	13	23
β-strand	53-54	2	7
β-strand	55	1	26
β-strand	58-64	7	25
β-strand	69-75	7	25
α-helix	78-80	3
β-strand	81-83	3	7
β-strand	93-98	6	23
β-strand	99	1	26
α-helix	102-105	4
β-strand	106-108	3	23
β-strand	115-120	6	25
β-strand	124-132	9	23
β-strand	137-138	2	23
β-strand	140-141	2	22

Chain G: 5 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	13-17	5
β-strand	20-25	6	27
α-helix	27-29	3
α-helix	33-35	3
β-strand	36-48	13	28
β-strand	53-54	2	16
β-strand	55	1	29
β-strand	58-64	7	27
β-strand	69-75	7	27
α-helix	78-80	3
β-strand	81-83	3	16
β-strand	93-98	6	28
β-strand	99	1	29
α-helix	102-105	4
β-strand	106-108	3	28
β-strand	115-120	6	27
β-strand	124-132	9	28
β-strand	137-138	2	28
β-strand	140-141	2	30

Chain H: 6 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
α-helix	13-16	4
β-strand	20-25	6	30
α-helix	27-29	3
α-helix	33-35	3
β-strand	36-48	13	28
β-strand	53-54	2	21
β-strand	55	1	31
β-strand	58-64	7	30
β-strand	69-75	7	30
α-helix	78-80	3
β-strand	81-82	2	21
β-strand	93-98	6	28
β-strand	99	1	31
α-helix	102-105	4
β-strand	106-108	3	28
β-strand	115-120	6	30
β-strand	124-132	9	28
β-strand	137-138	2	28
β-strand	140-141	2	27

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cationic trypsin	A, B, C, D	protein	223	Bos taurus	P00760 (AlphaFold model)
Ecotin	E, F, G, H	protein	142	Escherichia coli	P23827 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>4NIY_1 Cationic trypsin (chains A, B, C, D)
IVGGYTCGANTVPYQVSLNSGYHFCGGSLINSQWVVSAAHCYESGIQVRLGEDNINVVEG
NEQFISASKSIVHPSYNSNTLNNDIMLIKLKSAASLNSRVASISLPTSCASAGTQCLISG
WGHTKSSGTSHPDVLKCLKAPILSDSSCKSAYPGQITSNMFCAGYLEGGKKSCQGDSGGP
VVCSGKLQGIVSWGSGCAQKNKPGVYTKVCNYVSWIKQTIASN

Sequence of entity 2 (E, F, G, H), FASTA

>4NIY_2 Ecotin (chains E, F, G, H)
AESVQPLEKIAPYPQAEKGMKRQVIQLTPQEDESTLKVELLIGQTLEVDCNLHRLGGKLE
NKTLEGWGYDYYVFDKVSSPVSTYRHCPDGKKEKKFVTAYLGDAGMLRYNSKLPIVVYTP
DNVDVKYRVWKAEEKIDNAVVR

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	4
ZN	Zinc ion	Zn	1

Primary citation

N-terminal protein modification by substrate-activated reverse proteolysis. Liebscher, S., Schopfel, M., Aumuller, T. et al. Angew Chem Int Ed Engl (2014) 53:3024-3028. DOI 10.1002/anie.201307736 · 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)

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