Structure of PDB 8td9 Chain A

Receptor sequence

>8td9A (length=279) Species: 9606 (Homo sapiens)

YFQSMSVGFIGAGQLAFALAKGFTAAGVLAAHKIMASSPDMDLATVSALR
KMGVKLTPHNKETVQHSDVLFLAVKPHIIPFILDEIGADIEDRHIVVSCA
AGVTISSIEKKLSAFRPAPRVIRCMTNTPVVVREGATVYATGTHAQVEDG
RLMEQLLSSVGFCTEVEEDLIDAVTGLSGSGPAYAFTALDALADGGVKMG
LPRRLAVRLGAQALLGAAKMLLHSEQHPGQLKDNVSSPGGATIHALHVLE
SGGFRSLLINAVEASCIRTRELQSMADQE

3D structure

• PDB: 8td9 Screening a knowledge-based library of low molecular weight compounds against the proline biosynthetic enzyme 1-pyrroline-5-carboxylate 1 (PYCR1)
• Chain: A
• Resolution: 1.75 Å

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	NAI	A	G7 A8 G9 Q10 L11 S34 P35 L39 N56 A69 V70 I78 C95 A96 A97 M121 T124	G11 A12 G13 Q14 L15 S38 P39 L43 N60 A73 V74 I82 C99 A100 A101 M125 T128
BS02	YCP	A	V231 S233 T238	V235 S237 T242
BS03	YCP	A	A97 G175	A101 G179

Gene Ontology

Molecular Function

• GO:0004735 pyrroline-5-carboxylate reductase activity
• GO:0005515 protein binding
• GO:0016491 oxidoreductase activity
• GO:0042802 identical protein binding

Biological Process

• GO:0006561 proline biosynthetic process
• GO:0034599 cellular response to oxidative stress
• GO:0051881 regulation of mitochondrial membrane potential
• GO:0055129 L-proline biosynthetic process
• GO:1903377 negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway

Cellular Component

• GO:0005739 mitochondrion
• GO:0005759 mitochondrial matrix

External links

• PDB: RCSB:8td9, PDBe:8td9, PDBj:8td9
• PDBsum: 8td9
• PubMed: 39133178
• UniProt: P32322|P5CR1_HUMAN Pyrroline-5-carboxylate reductase 1, mitochondrial (Gene Name=PYCR1)