8GT7 | pdb_00008gt7

Structure of falcipain and human Stefin A mutant complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.28 Å
  • R-Value Free: 
    0.300 (Depositor), 0.282 (DCC) 
  • R-Value Work: 
    0.272 (Depositor), 0.274 (DCC) 
  • R-Value Observed: 
    0.275 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Structure of falcipain and human Stefin A complex

Chakraborty, S.Biswas, S.

To be published.

Macromolecule Content 

  • Total Structure Weight: 106.01 kDa 
  • Atom Count: 7,507 
  • Modeled Residue Count: 696 
  • Deposited Residue Count: 696 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cysteine proteinase falcipain 2a
A, C
241Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_1115700
EC: 3.4.22
UniProt
Find proteins for Q8I6U4 (Plasmodium falciparum (isolate 3D7))
Explore Q8I6U4 
Go to UniProtKB:  Q8I6U4
Entity Groups
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UniProt GroupQ8I6U4
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Cystatin-A
B, D
98Homo sapiensMutation(s): 1 
Gene Names: CSTASTF1STFA
UniProt & NIH Common Fund Data Resources
Find proteins for P01040 (Homo sapiens)
Explore P01040 
Go to UniProtKB:  P01040
PHAROS:  P01040
GTEx:  ENSG00000121552 
Entity Groups
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UniProt GroupP01040
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
LYS-GLU-ILE-VAL-ASN-PRO-LEU-THR-LYS9Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.22
UniProt
Find proteins for Q8I6U4 (Plasmodium falciparum (isolate 3D7))
Explore Q8I6U4 
Go to UniProtKB:  Q8I6U4
Entity Groups
UniProt GroupQ8I6U4
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
VAL-ASN-PRO-LEU-THR-LYS-LYS-GLY-GLU9Plasmodium falciparum 3D7Mutation(s): 0 
EC: 3.4.22
UniProt
Find proteins for Q8I6U4 (Plasmodium falciparum (isolate 3D7))
Explore Q8I6U4 
Go to UniProtKB:  Q8I6U4
Entity Groups
UniProt GroupQ8I6U4
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PE8
(Subject of Investigation/LOI)

Query on PE8



Download:Ideal Coordinates CCD File
BC [auth B]
CI [auth F]
GI [auth F]
JD [auth B]
KD [auth B]
BC [auth B],
CI [auth F],
GI [auth F],
JD [auth B],
KD [auth B],
LD [auth B],
OF [auth C],
UH [auth E],
VA [auth A],
VH [auth E],
WA [auth A],
XA [auth A]
3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL
C16 H34 O9
GLZWNFNQMJAZGY-UHFFFAOYSA-N
PG4
(Subject of Investigation/LOI)

Query on PG4



Download:Ideal Coordinates CCD File
AA [auth A]
AC [auth B]
AF [auth C]
AI [auth E]
BA [auth A]
AA [auth A],
AC [auth B],
AF [auth C],
AI [auth E],
BA [auth A],
BF [auth C],
BI [auth F],
CA [auth A],
CE [auth B],
CF [auth C],
DA [auth A],
DF [auth C],
DG [auth D],
EA [auth A],
EF [auth C],
FA [auth A],
FB [auth A],
FI [auth F],
HE [auth C],
PC [auth B],
PF [auth C],
QC [auth B],
QG [auth D],
QH [auth E],
RB [auth A],
RC [auth B],
RG [auth D],
RH [auth E],
SB [auth A],
SC [auth B],
SG [auth D],
SH [auth E],
TB [auth A],
TC [auth B],
TG [auth D],
UB [auth A],
UC [auth B],
UG [auth D],
VB [auth A],
VC [auth B],
WC [auth B],
XC [auth B],
Y [auth A],
YC [auth B],
YE [auth C],
Z [auth A],
ZE [auth C],
ZH [auth E]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PEG
(Subject of Investigation/LOI)

Query on PEG



Download:Ideal Coordinates CCD File
AD [auth B]
AH [auth D]
BD [auth B]
BH [auth D]
CD [auth B]
AD [auth B],
AH [auth D],
BD [auth B],
BH [auth D],
CD [auth B],
CH [auth D],
DD [auth B],
DE [auth B],
ED [auth B],
EE [auth B],
EG [auth D],
FD [auth B],
FE [auth B],
FG [auth D],
GB [auth A],
GD [auth B],
GF [auth C],
HD [auth B],
HF [auth C],
IA [auth A],
ID [auth B],
IE [auth C],
IF [auth C],
JA [auth A],
JF [auth C],
KA [auth A],
KF [auth C],
LA [auth A],
LF [auth C],
MA [auth A],
MD [auth B],
MF [auth C],
NA [auth A],
NF [auth C],
OA [auth A],
PA [auth A],
PD [auth B],
QA [auth A],
RA [auth A],
SA [auth A],
SF [auth C],
TA [auth A],
UA [auth A],
VG [auth D],
WB [auth A],
WG [auth D],
XB [auth A],
XG [auth D],
YB [auth A],
YG [auth D],
ZA [auth A],
ZC [auth B],
ZF [auth C],
ZG [auth D]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
FF [auth C],
GA [auth A],
GE [auth C],
HA [auth A],
TH [auth E]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
(Subject of Investigation/LOI)

Query on GOL



Download:Ideal Coordinates CCD File
AB [auth A]
AE [auth B]
AG [auth C]
BE [auth B]
CC [auth B]
AB [auth A],
AE [auth B],
AG [auth C],
BE [auth B],
CC [auth B],
DC [auth B],
DI [auth F],
EC [auth B],
FC [auth B],
FH [auth D],
G [auth A],
GC [auth B],
GG [auth D],
H [auth A],
HC [auth B],
HG [auth D],
I [auth A],
IC [auth B],
IG [auth D],
J [auth A],
JC [auth B],
JE [auth C],
JG [auth D],
K [auth A],
KC [auth B],
KE [auth C],
KG [auth D],
L [auth A],
LC [auth B],
LE [auth C],
LG [auth D],
LH [auth D],
M [auth A],
ME [auth C],
MG [auth D],
N [auth A],
ND [auth B],
NE [auth C],
NG [auth D],
NH [auth E],
O [auth A],
OB [auth A],
OE [auth C],
OH [auth E],
P [auth A],
PB [auth A],
PE [auth C],
PH [auth E],
Q [auth A],
QB [auth A],
QE [auth C],
QF [auth C],
R [auth A],
RE [auth C],
RF [auth C],
S [auth A],
SE [auth C],
T [auth A],
TE [auth C],
XF [auth C],
YA [auth A],
YF [auth C],
YH [auth E],
ZB [auth A],
ZD [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
(Subject of Investigation/LOI)

Query on EDO



Download:Ideal Coordinates CCD File
BG [auth D]
CG [auth D]
EB [auth A]
EH [auth D]
MH [auth E]
BG [auth D],
CG [auth D],
EB [auth A],
EH [auth D],
MH [auth E],
QD [auth B],
RD [auth B],
WH [auth E]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
BB [auth A]
CB [auth A]
DB [auth A]
DH [auth D]
EI [auth F]
BB [auth A],
CB [auth A],
DB [auth A],
DH [auth D],
EI [auth F],
GH [auth D],
HB [auth A],
HH [auth D],
HI [auth F],
IB [auth A],
IH [auth D],
JB [auth A],
JH [auth D],
KB [auth A],
KH [auth D],
LB [auth A],
MB [auth A],
MC [auth B],
NB [auth A],
NC [auth B],
OC [auth B],
OD [auth B],
OG [auth D],
PG [auth D],
SD [auth B],
TD [auth B],
TF [auth C],
U [auth A],
UD [auth B],
UE [auth C],
UF [auth C],
V [auth A],
VD [auth B],
VE [auth C],
VF [auth C],
W [auth A],
WD [auth B],
WE [auth C],
WF [auth C],
X [auth A],
XD [auth B],
XE [auth C],
XH [auth E],
YD [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.28 Å
  • R-Value Free:  0.300 (Depositor), 0.282 (DCC) 
  • R-Value Work:  0.272 (Depositor), 0.274 (DCC) 
  • R-Value Observed: 0.275 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.461α = 90
b = 119.62β = 90
c = 65.016γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentIndia--

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-13
    Type: Initial release
  • Version 1.1: 2025-09-17
    Changes: Advisory, Derived calculations, Structure summary