Structure of PDB 6lpt Chain B

Receptor sequence

>6lptB (length=467) Species: 9606 (Homo sapiens) [Search protein sequence]

PVRRLPFSTVSKQDLAAFERIVPGGVVTDPEALQAPNVDWLRTLRGCSKV
LLRPRTSEEVSHILRHCHERNLAVNPQGGNTGMVGGSVPVFDEIILSTAR
MNRVLSFHSVSGILVCQAGCVLEELSRYVEERDFIMPLDLGAKGSCHIGG
NVATNAGGLRFLRYGSLHGTVLGLEVVLADGTVLDCLTSLRKDNTGYDLK
QLFIGSEGTLGIITTVSILCPPKPRAVNVAFLGCPGFAEVLQTFSTCKGM
LGEILSAFEFMDAVCMQLVGRHLHLASPVQESPFYVLIETSGSNAGHDAE
KLGHFLEHALGSGLVTDGTMATDQRKVKMLWALRERITEALSRDGYVYKY
DLSLPVERLYDIVTDLRARLGPHAKHVVGYGHLGDGNLHLNVTAEAFSPS
LLAALEPHVYEWTAGQQGSVSAEHGVGFRKRDVLGYSKPPGALQLMQQLK
ALLDPKGILNPYKTLPS

3D structure

PDB

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

Chain

Resolution

2.621 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)	Binding affinity
BS01	FAD	B	W92 P128 G130 G131 N132 T133 G134 M135 G138 S139 L192 G193 A194 H199 N203 A205 T206 A208 G210 G260 I264 I265 E475 H476 N512	W40 P76 G78 G79 N80 T81 G82 M83 G86 S87 L140 G141 A142 H147 N151 A153 T154 A156 G158 G208 I212 I213 E423 H424 N460
BS02	ZN	B	H434 H441 E475	H382 H389 E423

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

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