Structure of PDB 6lpn Chain A

Receptor sequence
>6lpnA (length=466) Species: 9606 (Homo sapiens) [Search protein sequence]
VRRLPFSTVSKQDLAAFERIVPGGVVTDPEALQAPNVDWLRTLRGCSKVL
LRPRTSEEVSHILRHCHERNLAVNPQGGNTGMVGGSVPVFDEIILSTARM
NRVLSFHSVSGILVCQAGCVLEELSRYVEERDFIMPLDLGAKGSCHIGGN
VATNAGGLRFLRYGSLHGTVLGLEVVLADGTVLDCLTSLRKDNTGYDLKQ
LFIGSEGTLGIITTVSILCPPKPRAVNVAFLGCPGFAEVLQTFSTCKGML
GEILSAFEFMDAVCMQLVGRHLHLASPVQESPFYVLIETSGSNAGHDAEK
LGHFLEHALGSGLVTDGTMATDQRKVKMLWALRERITEALSRDGYVYKYD
LSLPVERLYDIVTDLRARLGPHAKHVVGYGHLGDGNLHLNVTAEAFSPSL
LAALEPHVYEWTAGQQGSVSAEHGVGFRKRDVLGYSKPPGALQLMQQLKA
LLDPKGILNPYKTLPS
3D structure
PDB6lpn Structure, substrate specificity, and catalytic mechanism of human D-2-HGDH and insights into pathogenicity of disease-associated mutations.
ChainA
Resolution2.206 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 A W92 P128 G130 G131 N132 T133 G134 G138 S139 L192 A194 C198 H199 G202 N203 A205 T206 A208 G260 I264 I265 E475 N512 W39 P75 G77 G78 N79 T80 G81 G85 S86 L139 A141 C145 H146 G149 N150 A152 T153 A155 G207 I211 I212 E422 N459
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6lpn, PDBe:6lpn, PDBj:6lpn
PDBsum6lpn
PubMed33431826
UniProtQ8N465|D2HDH_HUMAN D-2-hydroxyglutarate dehydrogenase, mitochondrial (Gene Name=D2HGDH)

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