8TD9

Structure of PYCR1 complexed with NADH and L-pipecolic acid

PDB DOI: https://doi.org/10.2210/pdb8TD9/pdb

Classification: OXIDOREDUCTASE/INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-07-02 Released: 2024-07-03
Deposition Author(s): Tanner, J.J., Meeks, K.R.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.207
R-Value Work: 0.182
R-Value Observed: 0.183

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Screening a knowledge-based library of low molecular weight compounds against the proline biosynthetic enzyme 1-pyrroline-5-carboxylate 1 (PYCR1)

Meeks, K.R., Bogner, A.N., Tanner, J.J.

(2024) Protein Sci 33

DOI: https://doi.org/10.1002/pro.5072

Macromolecule Content

Total Structure Weight: 172.12 kDa
Atom Count: 11,016
Modelled Residue Count: 1,391
Deposited Residue Count: 1,580
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pyrroline-5-carboxylate reductase 1, mitochondrial	A, B, C, D, E	316	Homo sapiens	Mutation(s): 0 Gene Names: PYCR1 EC: 1.5.1.2
UniProt & NIH Common Fund Data Resources
Find proteins for P32322 (Homo sapiens) Explore P32322 Go to UniProtKB: P32322
PHAROS: P32322 GTEx: ENSG00000183010
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P32322
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAI (Subject of Investigation/LOI) Query on NAI Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain O [auth D] SDF format, chain S [auth E] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain O [auth D] MOL2 format, chain S [auth E]	F [auth A], I [auth B], L [auth C], O [auth D], S [auth E]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C₂₁ H₂₉ N₇ O₁₄ P₂ BOPGDPNILDQYTO-NNYOXOHSSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D] Focus chain S [auth E] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Focus chain O [auth D] Focus chain S [auth E]
YCP (Subject of Investigation/LOI) Query on YCP Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain R [auth D] SDF format, chain T [auth E] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain R [auth D] MOL2 format, chain T [auth E]	H [auth A], K [auth B], N [auth C], R [auth D], T [auth E]	(2S)-piperidine-2-carboxylic acid C₆ H₁₁ N O₂ HXEACLLIILLPRG-YFKPBYRVSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain R [auth D] Focus chain T [auth E] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain R [auth D] Focus chain T [auth E]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain P [auth D] SDF format, chain Q [auth D] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D]	G [auth A], J [auth B], M [auth C], P [auth D], Q [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Focus chain Q [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Focus chain Q [auth D]