Macromolecule Content

Total Structure Weight: 106.64 kDa
Atom Count: 7153
Residue Count: 933
Unique protein chains: 1

6LPQ

Crystal structure of human D-2-hydroxyglutarate dehydrogenase in complex with D-malate (D-MAL)

DOI: 10.2210/pdb6LPQ/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-01-12 Released: 2021-01-13
Deposition Author(s): Yang, J., Zhu, H., Ding, J.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.255
R-Value Work: 0.215
R-Value Observed: 0.217

wwPDB Validation 3D Report Full Report

Literature

Crystal structure of human D-2-hydroxyglutarate dehydrogenase in complex with D-malate (D-MAL)

Yang, J., Zhu, H., Ding, J.

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-2-hydroxyglutarate dehydrogenase, mitochondrial	A, B	481	Homo sapiens	Mutation(s): 0 Gene Names: D2HGDH, D2HGD EC: 1.1.99
Find proteins for Q8N465 (Homo sapiens) Explore Q8N465 Go to UniProtKB: Q8N465
NIH Common Fund Data Resources
PHAROS Q8N465 GTEx ENSG00000180902
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain C [A] SDF format, chain F [B] MOL2 format, chain C [A] MOL2 format, chain F [B]	A, B	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Ligand Interaction
MLT Query on MLT Download Ideal Coordinates CCD File SDF format, chain E [A] SDF format, chain H [B] MOL2 format, chain E [A] MOL2 format, chain H [B]	A, B	D-MALATE C₄ H₆ O₅ BJEPYKJPYRNKOW-UWTATZPHSA-N		Ligand Interaction
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain D [A] SDF format, chain G [B] MOL2 format, chain D [A] MOL2 format, chain G [B]	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.255
R-Value Work: 0.215
R-Value Observed: 0.217
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.615	α = 90
b = 94.569	β = 111.55
c = 73.673	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Deposited Date: 2020-01-12
Released Date: 2021-01-13

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31870723
National Natural Science Foundation of China (NSFC)	China	31530013

Revision History

Version 1.0: 2021-01-13
Type: Initial release

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.