9PCT | pdb_00009pct

Structure of Porcine Trypsin Crystals Grown from PEG Complexed with Crystallization Additives III

PDB DOI: https://doi.org/10.2210/pdb9PCT/pdb

Classification: PEPTIDE BINDING PROTEIN
Organism(s): Sus scrofa
Expression System: Sus scrofa
Mutation(s): No

Deposited: 2025-06-29 Released: 2025-09-17
Deposition Author(s): McPherson, A.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.41 Å
R-Value Free:
0.170 (Depositor), 0.170 (DCC)
R-Value Work:
0.131 (Depositor), 0.131 (DCC)
R-Value Observed:
0.134 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

X-ray Diffraction Analyses of Trypsin Crystals Grown in the Presence of Additives

McPherson, A.

(2026) Cryst Growth Des 26: 352-364

DOI: https://doi.org/10.1021/acs.cgd.5c01305

Macromolecule Content

Total Structure Weight: 30.14 kDa
Atom Count: 2,252
Modeled Residue Count: 223
Deposited Residue Count: 231
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Trypsin	A	231	Sus scrofa	Mutation(s): 0 EC: 3.4.21.4
UniProt
Find proteins for P00761 (Sus scrofa) Explore P00761 Go to UniProtKB: P00761
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00761
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	B	2		N/A	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G05551OP GlyCosmos: G05551OP

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-2)-beta-D-fructofuranose	C [auth F]	2		N/A	Interactions Focus chain C [auth F] Interactions & Density Focus chain C [auth F]
Glycosylation Resources
GlyTouCan: G05551OP GlyCosmos: G05551OP

Small Molecules

Ligands 13 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG6 Query on PG6 Download:Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain FA [auth A] MOL2 format, chain O [auth A] MOL2 format, chain FA [auth A] mmCIF format, chain O [auth A] mmCIF format, chain FA [auth A]	FA [auth A], O [auth A]	1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE C₁₂ H₂₆ O₆ DMDPGPKXQDIQQG-UHFFFAOYSA-N		Interactions Focus chain FA [auth A] Focus chain O [auth A] Interactions & Density Focus chain FA [auth A] Focus chain O [auth A]
EPE (Subject of Investigation/LOI) Query on EPE Download:Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A]	P [auth A], Q [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain P [auth A] Focus chain Q [auth A] Interactions & Density Focus chain P [auth A] Focus chain Q [auth A]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain G [auth A] MOL2 format, chain J [auth A] MOL2 format, chain G [auth A] mmCIF format, chain J [auth A] mmCIF format, chain G [auth A]	G [auth A], J [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth A] Interactions & Density Focus chain G [auth A] Focus chain J [auth A]
FLC (Subject of Investigation/LOI) Query on FLC Download:Ideal Coordinates CCD File SDF format, chain LA [auth A] SDF format, chain F [auth A] MOL2 format, chain LA [auth A] MOL2 format, chain F [auth A] mmCIF format, chain LA [auth A] mmCIF format, chain F [auth A]	F [auth A], LA [auth A]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain F [auth A] Focus chain LA [auth A] Interactions & Density Focus chain F [auth A] Focus chain LA [auth A]
PG5 Query on PG5 Download:Ideal Coordinates CCD File SDF format, chain W [auth A] SDF format, chain L [auth A] SDF format, chain HA [auth A] SDF format, chain EA [auth A] SDF format, chain CA [auth A] MOL2 format, chain W [auth A] MOL2 format, chain L [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain CA [auth A] mmCIF format, chain W [auth A] mmCIF format, chain L [auth A] mmCIF format, chain HA [auth A] mmCIF format, chain EA [auth A] mmCIF format, chain CA [auth A]	CA [auth A], EA [auth A], HA [auth A], L [auth A], W [auth A]	1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE C₈ H₁₈ O₄ YFNKIDBQEZZDLK-UHFFFAOYSA-N		Interactions Focus chain CA [auth A] Focus chain EA [auth A] Focus chain HA [auth A] Focus chain L [auth A] Focus chain W [auth A] Interactions & Density Focus chain CA [auth A] Focus chain EA [auth A] Focus chain HA [auth A] Focus chain L [auth A] Focus chain W [auth A]
TAR (Subject of Investigation/LOI) Query on TAR Download:Ideal Coordinates CCD File SDF format, chain MA [auth A] MOL2 format, chain MA [auth A] mmCIF format, chain MA [auth A]	MA [auth A]	D(-)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-LWMBPPNESA-N		Interactions Focus chain MA [auth A] Interactions & Density Focus chain MA [auth A]
MLT (Subject of Investigation/LOI) Query on MLT Download:Ideal Coordinates CCD File SDF format, chain V [auth A] SDF format, chain N [auth A] SDF format, chain JA [auth A] MOL2 format, chain V [auth A] MOL2 format, chain N [auth A] MOL2 format, chain JA [auth A] mmCIF format, chain V [auth A] mmCIF format, chain N [auth A] mmCIF format, chain JA [auth A]	JA [auth A], N [auth A], V [auth A]	D-MALATE C₄ H₆ O₅ BJEPYKJPYRNKOW-UWTATZPHSA-N		Interactions Focus chain JA [auth A] Focus chain N [auth A] Focus chain V [auth A] Interactions & Density Focus chain JA [auth A] Focus chain N [auth A] Focus chain V [auth A]
BEN Query on BEN Download:Ideal Coordinates CCD File SDF format, chain U [auth A] SDF format, chain IA [auth A] SDF format, chain E [auth A] MOL2 format, chain U [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain E [auth A] mmCIF format, chain U [auth A] mmCIF format, chain IA [auth A] mmCIF format, chain E [auth A]	E [auth A], IA [auth A], U [auth A]	BENZAMIDINE C₇ H₈ N₂ PXXJHWLDUBFPOL-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain IA [auth A] Focus chain U [auth A] Interactions & Density Focus chain E [auth A] Focus chain IA [auth A] Focus chain U [auth A]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain Z [auth A] SDF format, chain Y [auth A] SDF format, chain M [auth A] SDF format, chain KA [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain GA [auth A] SDF format, chain BA [auth A] SDF format, chain AA [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain M [auth A] MOL2 format, chain KA [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain AA [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain M [auth A] mmCIF format, chain KA [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain GA [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain AA [auth A]	AA [auth A] BA [auth A] GA [auth A] H [auth A] I [auth A] AA [auth A], BA [auth A], GA [auth A], H [auth A], I [auth A], KA [auth A], M [auth A], Y [auth A], Z [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain GA [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain KA [auth A] Focus chain M [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain GA [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain KA [auth A] Focus chain M [auth A] Focus chain Y [auth A] Focus chain Z [auth A]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain S [auth A] MOL2 format, chain S [auth A] mmCIF format, chain S [auth A]	S [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain S [auth A] Interactions & Density Focus chain S [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain X [auth A] SDF format, chain K [auth A] MOL2 format, chain X [auth A] MOL2 format, chain K [auth A] mmCIF format, chain X [auth A] mmCIF format, chain K [auth A]	K [auth A], X [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain X [auth A] Interactions & Density Focus chain K [auth A] Focus chain X [auth A]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain T [auth A] SDF format, chain R [auth A] SDF format, chain DA [auth A] MOL2 format, chain T [auth A] MOL2 format, chain R [auth A] MOL2 format, chain DA [auth A] mmCIF format, chain T [auth A] mmCIF format, chain R [auth A] mmCIF format, chain DA [auth A]	DA [auth A], R [auth A], T [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain DA [auth A] Focus chain R [auth A] Focus chain T [auth A] Interactions & Density Focus chain DA [auth A] Focus chain R [auth A] Focus chain T [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]