4DOQ: Trypsin

Crystal structure of the complex of Porcine Pancreatic Trypsin with 1/2SLPI. Determined by X-ray diffraction at 2.0 Å resolution. Released 14 Aug 2013.

Method: X-ray diffraction
Resolution: 2.0 Å
Organisms: Sus scrofa, Homo sapiens
Chains: 5
Atoms: 6,178
Mol. weight: 82.29 kDa
Ligands: CA, XPE
Released: 14 Aug 2013

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

Secondary structure: helices and β-sheets

4DOQ contains 33 α-helices and 68 β-strands across 5 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 A: 9 helices, 20 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	64-67	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
α-helix	111-113	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
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	204-216	9	2
β-strand	226-230	5	2
α-helix	231-234	4
α-helix	235-243	9

Chain B: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	63	1	6
α-helix	64-66	3
β-strand	70-71	2	2
α-helix	83-85	3
β-strand	91-95	5	7
β-strand	98-102	5	7
β-strand	105	1	6

Chain C: 10 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	17	1	8
β-strand	20-21	2	9
α-helix	22-23	2
β-strand	30-34	5	10
β-strand	40-48	9	10
β-strand	51-54	4	10
α-helix	56-58	3
α-helix	63	1
β-strand	64-67	4	10
β-strand	72	1	11
β-strand	81-90	10	10
β-strand	95	1	12
β-strand	100	1	12
β-strand	104-108	5	10
β-strand	122	1	9
α-helix	123-124	2
α-helix	128-130	3
β-strand	135-140	6	9
β-strand	154	1	11
α-helix	155	1
β-strand	156-162	7	9
α-helix	163-164	2
α-helix	165-171	7
β-strand	180-183	4	9
β-strand	189	1	8
β-strand	198-201	4	9
β-strand	204-216	9	9
β-strand	226-230	5	9
α-helix	231-234	4
α-helix	235-243	9

Chain D: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	63	1	13
α-helix	64-66	3
β-strand	70-71	2	9
α-helix	83-85	3
β-strand	91-95	5	14
β-strand	98-102	5	14
α-helix	103-104	2
β-strand	105	1	13

Chain E: 9 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	40-48	9	17
β-strand	51-54	4	17
α-helix	56-58	3
β-strand	64-67	4	17
β-strand	71	1	18
β-strand	80-89	10	17
β-strand	103-107	5	17
β-strand	121	1	16
α-helix	122-123	2
α-helix	128-130	3
β-strand	135-140	6	16
β-strand	154	1	18
α-helix	155	1
β-strand	156-162	7	16
α-helix	163-164	2
α-helix	165-171	7
β-strand	180-183	4	16
β-strand	189	1	15
β-strand	198-201	4	16
β-strand	204-215	8	16
β-strand	226-230	5	16
α-helix	231-234	4
α-helix	235-244	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Trypsin	A, C, E	protein	223	Sus scrofa	P00761 (AlphaFold model)
Antileukoproteinase	B, D	protein	47	Homo sapiens	P03973 (AlphaFold model)

Sequence of entity 1 (A, C, E), FASTA

>4DOQ_1 Trypsin (chains A, C, E)
IVGGYTCAANSIPYQVSLNSGSHFCGGSLINSQWVVSAAHCYKSRIQVRLGEHNIDVLEG
NEQFINAAKIITHPNFNGNTLDNDIMLIKLSSPATLNSRVATVSLPRSCAAAGTECLISG
WGNTKSSGSSYPSLLQCLKAPVLSDSSCKSSYPGQITGNMICVGFLEGGKDSCQGDSGGP
VVCNGQLQGIVSWGYGCAQKNKPGVYTKVCNYVNWIQQTIAAN

Sequence of entity 2 (B, D), FASTA

>4DOQ_2 Antileukoproteinase (chains B, D)
KPGKCPVTYGQCLMLNPPNFCEMDGQCKRDLKCCMGMCGKSCVSPVK

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	3
XPE	3,6,9,12,15,18,21,24,27-nonaoxanonacosane-1,29-diol	C20 H42 O11	1

Water and common crystallization additives (P6G, SO4) are not listed.

Primary citation

Structure basis 1/2SLPI and porcine pancreas trypsin interaction. Fukushima, K., Kamimura, T., Takimoto-Kamimura, M. J Synchrotron Radiat (2013) 20:943-947. DOI 10.1107/S090904951302133X · PubMed

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

9PDA 1.18 Å, Structure of Porcine Trypsin Crystals Grown From PEG and Complexed With Crystallization…
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…

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