Structure of PDB 8td2 Chain B

Receptor sequence

>8td2B (length=281) Species: 9606 (Homo sapiens)

NLYFQSMSVGFIGAGQLAFALAKGFTAAGVLAAHKIMASSPDMDLATVSA
LRKMGVKLTPHNKETVQHSDVLFLAVKPHIIPFILDEIGADIEDRHIVVS
CAAGVTISSIEKKLSAFRPAPRVIRCMTNTPVVVREGATVYATGTHAQVE
DGRLMEQLLSSVGFCTEVEEDLIDAVTGLSGSGPAYAFTALDALADGGVK
MGLPRRLAVRLGAQALLGAAKMLLHSEQHPGQLKDNVSSPGGATIHALHV
LESGGFRSLLINAVEASCIRTRELQSMADQE

3D structure

• PDB: 8td2 Screening a knowledge-based library of low molecular weight compounds against the proline biosynthetic enzyme 1-pyrroline-5-carboxylate 1 (PYCR1)
• Chain: B
• Resolution: 1.65 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	B	A8 G9 Q10 L11 P35 L39 N56 A69 V70 K71 P72 I74 I78 C95 A96 A97 M121 T122 T124	A14 G15 Q16 L17 P41 L45 N62 A75 V76 K77 P78 I80 I84 C101 A102 A103 M127 T128 T130
BS02	ZPS	B	V231 S233 A237 T238	V237 S239 A243 T244

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:8td2, PDBe:8td2, PDBj:8td2
• PDBsum: 8td2
• PubMed: 39133178
• UniProt: P32322|P5CR1_HUMAN Pyrroline-5-carboxylate reductase 1, mitochondrial (Gene Name=PYCR1)