9PDA: Porcine Trypsin Crystals Grown From PEG and

Structure of Porcine Trypsin Crystals Grown From PEG and Complexed With Crystallization Additives IV. Determined by X-ray diffraction at 1.18 Å resolution. Released 24 Sept 2025.

Method: X-ray diffraction
Resolution: 1.18 Å
Organism: Sus scrofa
Chains: 4
Atoms: 8,920
Mol. weight: 112.92 kDa
Ligands: BEN, PG5, PG6, CA
Released: 24 Sept 2025

Explore 9PDA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9PDA contains 36 α-helices and 76 β-strands across 4 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: 9 helices, 18 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	38-46	9	3
β-strand	49-52	4	3
α-helix	54-56	3
β-strand	62-65	4	3
β-strand	69	1	4
β-strand	78-87	10	3
β-strand	101-105	5	3
α-helix	108-111	4
β-strand	119	1	2
α-helix	120-121	2
α-helix	124-126	3
β-strand	130-135	6	2
β-strand	149	1	4
β-strand	151-157	7	2
α-helix	158-159	2
α-helix	160-166	7
β-strand	175-178	4	2
β-strand	186	1	1
β-strand	195-198	4	2
β-strand	201-208	8	2
β-strand	219-223	5	2
α-helix	224-227	4
α-helix	228-236	9

Chain B: 10 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	5
β-strand	20-21	2	6
α-helix	22-23	2
β-strand	30-34	5	7
β-strand	38-46	9	7
β-strand	49-52	4	7
α-helix	54-56	3
β-strand	62-65	4	7
β-strand	69	1	8
β-strand	78-87	10	7
β-strand	101-105	5	7
α-helix	108-111	4
β-strand	112	1	9
β-strand	115	1	9
β-strand	119	1	6
α-helix	120-121	2
α-helix	124-126	3
β-strand	130-135	6	6
β-strand	149	1	8
α-helix	150	1
β-strand	151-157	7	6
α-helix	158-159	2
α-helix	160-166	7
β-strand	175-178	4	6
β-strand	186	1	5
β-strand	195-198	4	6
β-strand	201-208	8	6
β-strand	214	1	10
β-strand	217	1	10
β-strand	219-223	5	6
α-helix	224-226	3
α-helix	228-237	10

Chain D: 8 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	15
β-strand	20-21	2	16
α-helix	22-23	2
β-strand	30-34	5	17
β-strand	38-46	9	17
β-strand	49-52	4	17
α-helix	54-56	3
β-strand	62-65	4	17
β-strand	69	1	18
β-strand	78-87	10	17
β-strand	101-105	5	17
β-strand	119	1	16
α-helix	120-121	2
α-helix	124-126	3
β-strand	130-135	6	16
β-strand	149	1	18
β-strand	151-157	7	16
α-helix	158-159	2
α-helix	160-166	7
β-strand	175-178	4	16
β-strand	186	1	15
β-strand	195-198	4	16
β-strand	201-208	8	16
β-strand	219-223	5	16
α-helix	224-226	3
α-helix	228-237	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Trypsin	A, B, C, D	protein	231	Sus scrofa	P00761 (AlphaFold model)

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

>9PDA_1 Trypsin (chains A, B, C, D)
FPTDDDDKIVGGYTCAANSIPYQVSLNSGSHFCGGSLINSQWVVSAAHCYKSRIQVRLGE
HNIDVLEGNEQFINAAKIITHPNFNGNTLDNDIMLIKLSSPATLNSRVATVSLPRSCAAA
GTECLISGWGNTKSSGSSYPSLLQCLKAPVLSDSSCKSSYPGQITGNMICVGFLEGGKDS
CQGDSGGPVVCNGQLQGIVSWGYGCAQKNKPGVYTKVCNYVNWIQQTIAAN

Ligands and cofactors

ID	Name	Formula	Copies
BEN	Benzamidine	C7 H8 N2	10
PG5	1-methoxy-2-[2-(2-methoxy-ethoxy]-ethane	C8 H18 O4	12
PG6	1-(2-methoxy-ethoxy)-2-{2-[2-(2-methoxy-ethoxy]-ethoxy}-ethane	C12 H26 O6	1
CA	Calcium ion	Ca	5
MLI	Malonate ion	C3 H2 O4	4
PMA	Pyromellitic acid	C10 H6 O8	2

Water and common crystallization additives (PEG, PG4, EPE, CL) are not listed.

Primary citation

X-ray Diffraction Analyses of Trypsin Crystals Grown in the Presence of Additives. McPherson, A. Cryst Growth Des (2026) 26:352-364. DOI 10.1021/acs.cgd.5c01305

Other PDB entries of the same protein (UniProt P00761 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1S83 1.25 Å, Porcine trypsin complexed with 4-amino propanol
2A31 1.25 Å, Trypsin in complex with borate
9PDC 1.27 Å, Porcine Trypsin grown from PEG and Complexed with Crystallization Additives II
9PD9 1.28 Å, The Structure of Porcine Trypsin in Complex with Crystallization Additives I
1S5S 1.4 Å, Porcine trypsin complexed with guanidine-3-propanol inhibitor
9PCT 1.41 Å, Structure of Porcine Trypsin Crystals Grown from PEG Complexed with Crystallization…
1S6H 1.45 Å, Porcine trypsin complexed with guanidine-3-propanol inhibitor
1H9H 1.5 Å, Complex of eeti-II with porcine trypsin
2A32 1.5 Å, Trypsin in complex with benzene boronic acid
1FNI 1.6 Å, Crystal structure of porcine beta trypsin with 0.01% polydocanol
1MCT 1.6 Å, The refined 1.6 Å resolution crystal structure of the complex formed between porcine…
1QQU 1.63 Å, Crystal structure of porcine beta trypsin with bound acetate ion

Browse structure collections

About this viewer

MolViewer shows 9PDA 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.