6E90

Ternary complex of human glycerol 3-phosphate dehydrogenase

  • Classification: OXIDOREDUCTASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli

  • Deposited: 2018-07-31 Released: 2019-01-30 
  • Deposition Author(s): Mydy, L.S., Gulick, A.M.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases; National Institutes of Health/National Institute of General Medical Sciences 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Human Glycerol 3-Phosphate Dehydrogenase: X-Ray Crystal Structures that Guide the Interpretation of Mutagenesis Studies.

Mydy, L.S.Cristobal, J.R.Katigbak, R.D.Bauer, P.Reyes, A.C.Kamerlin, S.C.L.Richard, J.P.Gulick, A.M.

(2019) Biochemistry --: --


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycerol-3-phosphate dehydrogenase [NAD(+)], cytoplasmic
A, B, C, D
349Homo sapiensMutation(s): 0 
Gene Names: GPD1
EC: 1.1.1.8
Find proteins for P21695 (Homo sapiens)
Go to Gene View: GPD1
Go to UniProtKB:  P21695
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

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Download CCD File 
C, D
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
13P
Query on 13P

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Download CCD File 
A, B
1,3-DIHYDROXYACETONEPHOSPHATE
C3 H7 O6 P
GNGACRATGGDKBX-UHFFFAOYSA-N
 Ligand Interaction
NAD
Query on NAD

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Download CCD File 
A, B, C
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
MPD
Query on MPD

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Download CCD File 
A, D
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.177 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 58.940α = 63.87
b = 79.560β = 86.60
c = 85.060γ = 83.61
Software Package:
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI116998
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM116921

Revision History 

  • Version 1.0: 2019-01-30
    Type: Initial release