Structure of PDB 6lpq Chain A

Receptor sequence

>6lpqA (length=466) Species: 9606 (Homo sapiens) [Search protein sequence]

VRRLPFSTVSKQDLAAFERIVPGGVVTDPEALQAPNVDWLRTLRGCSKVL
LRPRTSEEVSHILRHCHERNLAVNPQGGNTGMVGGSVPVFDEIILSTARM
NRVLSFHSVSGILVCQAGCVLEELSRYVEERDFIMPLDLGAKGSCHIGGN
VATNAGGLRFLRYGSLHGTVLGLEVVLADGTVLDCLTSLRKDNTGYDLKQ
LFIGSEGTLGIITTVSILCPPKPRAVNVAFLGCPGFAEVLQTFSTCKGML
GEILSAFEFMDAVCMQLVGRHLHLASPVQESPFYVLIETSGSNAGHDAEK
LGHFLEHALGSGLVTDGTMATDQRKVKMLWALRERITEALSRDGYVYKYD
LSLPVERLYDIVTDLRARLGPHAKHVVGYGHLGDGNLHLNVTAEAFSPSL
LAALEPHVYEWTAGQQGSVSAEHGVGFRKRDVLGYSKPPGALQLMQQLKA
LLDPKGILNPYKTLPS

3D structure

PDB

6lpq Structure, substrate specificity, and catalytic mechanism of human D-2-HGDH and insights into pathogenicity of disease-associated mutations.

Chain

Resolution

2.8 Å

3D
structure

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Enzymatic activity

Enzyme Commision number

1.1.99.39: D-2-hydroxyglutarate dehydrogenase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)
BS01	FAD	A	W92 P128 G130 G131 N132 T133 G134 G138 S139 L192 G193 A194 C198 H199 G202 N203 A205 T206 A208 G210 E259 G260 I264 I265 E475 N512	W39 P75 G77 G78 N79 T80 G81 G85 S86 L139 G140 A141 C145 H146 G149 N150 A152 T153 A155 G157 E206 G207 I211 I212 E422 N459
BS02	ZN	A	H434 H441 E475	H381 H388 E422
BS03	MLT	A	M135 R386 T390 K401 Y432 H434 H441 E475 H476	M82 R333 T337 K348 Y379 H381 H388 E422 H423

Gene Ontology

	Molecular Function
GO:0003824	catalytic activity
GO:0008270	zinc ion binding
GO:0016491	oxidoreductase activity
GO:0046872	metal ion binding
GO:0050660	flavin adenine dinucleotide binding
GO:0051990	(R)-2-hydroxyglutarate dehydrogenase activity
GO:0071949	FAD binding

	Biological Process
GO:0006103	2-oxoglutarate metabolic process
GO:0006108	malate metabolic process
GO:0010042	response to manganese ion
GO:0010043	response to zinc ion
GO:0019538	protein metabolic process
GO:0032025	response to cobalt ion
GO:0032026	response to magnesium ion
GO:0051592	response to calcium ion

	Cellular Component
GO:0005739	mitochondrion
GO:0005759	mitochondrial matrix

View graph for
Molecular Function

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Biological Process

View graph for
Cellular Component

External links

PDB	RCSB:6lpq, PDBe:6lpq, PDBj:6lpq
PDBsum	6lpq
PubMed	33431826
UniProt	Q8N465\|D2HDH_HUMAN D-2-hydroxyglutarate dehydrogenase, mitochondrial (Gene Name=D2HGDH)

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