9PDA | pdb_00009pda

Structure of Porcine Trypsin Crystals Grown From PEG and Complexed With Crystallization Additives IV


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.18 Å
  • R-Value Free: 
    0.230 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.195 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

Starting Model: experimental
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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

Macromolecule Content 

  • Total Structure Weight: 112.92 kDa 
  • Atom Count: 8,920 
  • Modeled Residue Count: 892 
  • Deposited Residue Count: 924 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Trypsin
A, B, C, D
231Sus scrofaMutation(s): 0 
EC: 3.4.21.4
UniProt
Find proteins for P00761 (Sus scrofa)
Explore P00761 
Go to UniProtKB:  P00761
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00761
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG6

Query on PG6



Download:Ideal Coordinates CCD File
G [auth A]1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE
C12 H26 O6
DMDPGPKXQDIQQG-UHFFFAOYSA-N
PMA
(Subject of Investigation/LOI)

Query on PMA



Download:Ideal Coordinates CCD File
FC [auth D],
Y [auth B]
PYROMELLITIC ACID
C10 H6 O8
CYIDZMCFTVVTJO-UHFFFAOYSA-N
EPE

Query on EPE



Download:Ideal Coordinates CCD File
EB [auth C],
IC [auth D]
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
PG4

Query on PG4



Download:Ideal Coordinates CCD File
AB [auth B]
AC [auth C]
BC [auth C]
FD [auth D]
GD [auth D]
AB [auth B],
AC [auth C],
BC [auth C],
FD [auth D],
GD [auth D],
HD [auth D],
ID [auth D],
JD [auth D],
KD [auth D],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
XB [auth C],
YA [auth B],
YB [auth C],
ZA [auth B],
ZB [auth C]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PG5

Query on PG5



Download:Ideal Coordinates CCD File
BA [auth B]
DA [auth B]
F [auth A]
GB [auth C]
GC [auth D]
BA [auth B],
DA [auth B],
F [auth A],
GB [auth C],
GC [auth D],
H [auth A],
HA [auth B],
HB [auth C],
HC [auth D],
I [auth A],
PC [auth D],
XA [auth B]
1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE
C8 H18 O4
YFNKIDBQEZZDLK-UHFFFAOYSA-N
BEN

Query on BEN



Download:Ideal Coordinates CCD File
AA [auth B]
CB [auth C]
DB [auth C]
E [auth A]
EC [auth D]
AA [auth B],
CB [auth C],
DB [auth C],
E [auth A],
EC [auth D],
IB [auth C],
JC [auth D],
MC [auth D],
X [auth B],
Z [auth B]
BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
AD [auth D]
BB [auth B]
BD [auth D]
CA [auth B]
CC [auth C]
AD [auth D],
BB [auth B],
BD [auth D],
CA [auth B],
CC [auth C],
CD [auth D],
DC [auth C],
DD [auth D],
EA [auth B],
ED [auth D],
FA [auth B],
FB [auth C],
GA [auth B],
IA [auth B],
J [auth A],
JA [auth B],
JB [auth C],
K [auth A],
KA [auth B],
KB [auth C],
KC [auth D],
L [auth A],
LA [auth B],
LB [auth C],
LC [auth D],
LD [auth D],
M [auth A],
MA [auth B],
MB [auth C],
MD [auth D],
NA [auth B],
NB [auth C],
NC [auth D],
ND [auth D],
OA [auth B],
OB [auth C],
OC [auth D],
OD [auth D],
P [auth A],
PA [auth B],
Q [auth A],
R [auth A],
RB [auth C],
SA [auth B],
SB [auth C],
TA [auth B],
TB [auth C],
TC [auth D],
UA [auth B],
UB [auth C],
UC [auth D],
VA [auth B],
VB [auth C],
VC [auth D],
W [auth A],
WA [auth B],
WB [auth C],
WC [auth D],
XC [auth D],
YC [auth D],
ZC [auth D]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
MLI

Query on MLI



Download:Ideal Coordinates CCD File
O [auth A],
QB [auth C],
RA [auth B],
SC [auth D]
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
CA

Query on CA



Download:Ideal Coordinates CCD File
N [auth A],
PB [auth C],
QA [auth B],
QC [auth D],
RC [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
PD [auth D]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.18 Å
  • R-Value Free:  0.230 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.195 (Depositor), 0.195 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.66α = 90
b = 50.72β = 99.52
c = 125.69γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
d*TREKdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-24
    Type: Initial release
  • Version 1.1: 2026-05-27
    Changes: Database references