Structure of PDB 7p0m Chain D Binding Site BS03

Receptor Information

>7p0m Chain D (length=531) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

EKDDKDAIEEKFRERLKELVVPKHVMDVVDEELSKLGLLDNHSSEFNVTR
NYLDWLTSIPWGKYSNENLDLARAQAVLEEDHYGMEDVKKRILEFIAVSQ
LRGSTQGKILCFYGPPGVGKTSIARSIARALNREYFRFSVGGMTDVAEIK
GHRRTYVGAMPGKIIQCLKKTKTENPLILIDEVDKIGRGYQGDPSSALLE
LLDPEQNANFLDHYLDVPVDLSKVLFICTANVTDTIPEPLRDRMEMINVS
GYVAQEKLAIAERYLVPQARALCGLDESKAKLSSDVLTLLIKQYCRESGV
RNLQKQVEKVLRKSAYKIVSGEAESVEVTPENLQDFVGKPVFTVERMYDV
TPPGVVMGLAWTAMGGSTLFVETSLRRKDGSLEVTGQLGEVMKESARIAY
TFARAFLMQHAPANDYLVTSHIHLHVPEGATPKDGPSAGCTIVTALLSLA
MGRPVRQNLAMTGEVSLTGKILPVGGIKEATIAAKRAGVTCIVLPAENKK
DFYDLAAFITEGLEVHFVEHYREIFDIAFPD

Ligand information

Ligand ID

ADP

InChI

InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1

InChIKey

XTWYTFMLZFPYCI-KQYNXXCUSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.5.0	c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341	Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04	O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
CACTVS 3.341	Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
OpenEye OEToolkits 1.5.0	c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N

Formula

C10 H15 N5 O10 P2

Name

ADENOSINE-5'-DIPHOSPHATE

PDB chain

7p0m Chain D Residue 1001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	7p0m A dual allosteric pathway drives human mitochondrial Lon
Resolution	2.75 Å
Binding residue (original residue number in PDB)	Y492 G526 V527 G528 K529 T530 S531 Y661 I669 Y673 V709 R710
Binding residue (residue number reindexed from 1)	Y83 G117 V118 G119 K120 T121 S122 Y252 I260 Y264 V300 R301
Annotation score	5

Enzymatic activity

Enzyme Commision number

3.4.21.53: endopeptidase La.

Gene Ontology

	Molecular Function
GO:0001018	mitochondrial promoter sequence-specific DNA binding
GO:0003677	DNA binding
GO:0003697	single-stranded DNA binding
GO:0003727	single-stranded RNA binding
GO:0004176	ATP-dependent peptidase activity
GO:0004252	serine-type endopeptidase activity
GO:0005515	protein binding
GO:0005524	ATP binding
GO:0008236	serine-type peptidase activity
GO:0016887	ATP hydrolysis activity
GO:0042731	PH domain binding
GO:0042802	identical protein binding
GO:0043531	ADP binding
GO:0043560	insulin receptor substrate binding
GO:0043565	sequence-specific DNA binding
GO:0051880	G-quadruplex DNA binding
GO:0070182	DNA polymerase binding

	Biological Process
GO:0000002	mitochondrial genome maintenance
GO:0001666	response to hypoxia
GO:0006508	proteolysis
GO:0006515	protein quality control for misfolded or incompletely synthesized proteins
GO:0007005	mitochondrion organization
GO:0030163	protein catabolic process
GO:0032042	mitochondrial DNA metabolic process
GO:0034599	cellular response to oxidative stress
GO:0035694	mitochondrial protein catabolic process
GO:0046627	negative regulation of insulin receptor signaling pathway
GO:0051131	chaperone-mediated protein complex assembly
GO:0051603	proteolysis involved in protein catabolic process
GO:0070407	oxidation-dependent protein catabolic process

	Cellular Component
GO:0005654	nucleoplasm
GO:0005739	mitochondrion
GO:0005759	mitochondrial matrix
GO:0005829	cytosol
GO:0016020	membrane
GO:0042645	mitochondrial nucleoid

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External links

PDB	RCSB:7p0m, PDBe:7p0m, PDBj:7p0m
PDBsum	7p0m
PubMed
UniProt	P36776\|LONM_HUMAN Lon protease homolog, mitochondrial (Gene Name=LONP1)

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