1J16: Benzamidine

Benzamidine in complex with rat trypsin mutant X99/175/190RT. Determined by X-ray diffraction at 1.6 Å resolution. Released 23 Dec 2002.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Rattus norvegicus
Chains: 1
Atoms: 2,003
Mol. weight: 24.74 kDa
Ligands: BEN, CA
Released: 23 Dec 2002

Explore 1J16 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1J16 contains 8 α-helices and 22 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: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	1
β-strand	20-21	2	2
α-helix	22-23	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	64-68	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	115	1	6
β-strand	118	1	6
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	156-163	8	2
α-helix	165-169	5
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	226-230	5	2
α-helix	231-234	4
α-helix	235-244	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Trypsin II, anionic	A	protein	223	Rattus norvegicus	P00763 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1J16_1 Trypsin II, anionic (chains A)
IVGGYTCQENSVPYQVSLNSGYHFCGGSLINDQWVVSAAHCYKSRIQVRLGEHNINVLEG
NEQFVNAAKIIKHPNFDRETYNNDIMLIKLSSPVKLNARVATVALPSSCAPAGTQCLISG
WGNTLSSGVNEPDLLQCLDAPLLPQADCEASSSFIITDNMVCVGFLEGGKDACQGDSGGP
VVCNGELQGIVSWGYGCALPDNPGVYTKVCNYVDWIQDTIAAN

Ligands and cofactors

ID	Name	Formula	Copies
BEN	Benzamidine	C7 H8 N2	4
CA	Calcium ion	Ca	1

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

Primary citation

Reconstructing the Binding Site of Factor Xa in Trypsin Reveals Ligand-induced Structural Plasticity. Reyda, S., Sohn, C., Klebe, G. et al. J Mol Biol (2003) 325:963-977. DOI 10.1016/S0022-2836(02)01337-2 · PubMed

Other PDB entries of the same protein (UniProt P00763 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3FP7 1.46 Å, Anionic trypsin variant S195A in complex with bovine pancreatic trypsin inhibitor (BPTI)…
3FP8 1.46 Å, Anionic trypsin variant S195A in complex with bovine pancreatic trypsin inhibitor (BPTI)…
3FP6 1.49 Å, Anionic trypsin in complex with bovine pancreatic trypsin inhibitor (BPTI) determined to…
1F7Z 1.55 Å, Rat trypsinogen K15A complexed with bovine pancreatic trypsin inhibitor
1DPO 1.59 Å, Structure of rat trypsin
1F5R 1.65 Å, Rat trypsinogen mutant complexed with bovine pancreatic trypsin inhibitor
1FY8 1.7 Å, Crystal structure of the DELTAILE16VAL17 rat anionic trypsinogen-bpti complex
1YKT 1.7 Å, Trypsin/Bpti complex mutant
1YLC 1.7 Å, Trypsin/BPTI complex mutant
1YLD 1.7 Å, Trypsin/BPTI complex mutant
3TGK 1.7 Å, Trypsinogen mutant D194N and deletion of ile 16-val 17 complexed with bovine pancreatic…
1SLU 1.8 Å, Rat anionic N143H, E151H trypsin complexed to A86H ecotin

Browse structure collections

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