8ZMU

GLUTAMATE DEHYDROGENASE (W89F-MUTANT) FROM THERMOCOCCUS PROFUNDUS IN THE UNLIGANDED STATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Mechanism for drastic reduction in catalytic activity of Trp89Phe-mutated glutamate dehydrogenase revealed by cryoEM-sampling metastable conformation in action

Wakabayashi, T.Matsui, Y.Nakasako, M.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamate dehydrogenase
A, B, C, D, E
A, B, C, D, E, F
419Thermococcus profundusMutation(s): 1 
Gene Names: gdhAgdh
EC: 1.4.1.3
UniProt
Find proteins for O74024 (Thermococcus profundus)
Explore O74024 
Go to UniProtKB:  O74024
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO74024
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AB [auth D]
BB [auth D]
CB [auth E]
DB [auth E]
EB [auth E]
AB [auth D],
BB [auth D],
CB [auth E],
DB [auth E],
EB [auth E],
FA [auth C],
FB [auth E],
G [auth A],
GA [auth C],
GB [auth E],
H [auth A],
HA [auth C],
HB [auth E],
I [auth A],
IA [auth C],
IB [auth E],
J [auth A],
JA [auth C],
K [auth A],
KA [auth C],
L [auth A],
LA [auth C],
M [auth A],
MA [auth C],
MB [auth F],
N [auth A],
NA [auth C],
NB [auth F],
O [auth A],
OB [auth F],
P [auth A],
PB [auth F],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
WA [auth D],
X [auth B],
XA [auth D],
Y [auth B],
YA [auth D],
Z [auth B],
ZA [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
CA [auth B]
DA [auth B]
KB [auth E]
LB [auth E]
RA [auth C]
CA [auth B],
DA [auth B],
KB [auth E],
LB [auth E],
RA [auth C],
S [auth A],
SA [auth C],
TA [auth C],
UA [auth C],
VA [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACY
Query on ACY

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
JB [auth E]
OA [auth C]
PA [auth C]
AA [auth B],
BA [auth B],
JB [auth E],
OA [auth C],
PA [auth C],
Q [auth A],
QA [auth C],
R [auth A]
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
EA [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.355α = 90
b = 163.248β = 113.91
c = 132.605γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japanjp13480214
Japan Society for the Promotion of Science (JSPS)Japanjp19204042
Japan Society for the Promotion of Science (JSPS)Japanjp22244054
Japan Society for the Promotion of Science (JSPS)Japanjp21H01050
Japan Society for the Promotion of Science (JSPS)Japanjp26800227
Japan Society for the Promotion of Science (JSPS)Japan18J11653
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japanjp15076210
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japanjp20050030
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japanjp22018027
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japanjp23120525
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japanjp25120725
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japanjp15H01647
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japanjp17H05891

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-05
    Type: Initial release