MolNFT v1 · #135832 · protein
Structure of human pycr-1 complexed with NADPH
5UAT · Pyrroline-5-carboxylate reductase 1, mitochondrial: “Structure of human pycr-1 complexed with NADPH”. X-ray diffraction, 2 ligands (NDP, SO4), 10 pockets (best druggability 0.76). MolNFT v1 #135832 on GenesisL1: 3D structure…
- PDB
- 5UAT
- Type
- protein
- Length
- 1,373 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyrroline-5-carboxylate reductase 1, mitochondrial
- EC
- 1.5.1.2
- UniProt
- P32322
- Ligands
- NDP, SO4
- Pockets
- 10 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 60% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyrroline-5-carboxylate reductase 1, mitochondrial (EC 1.5.1.2) | protein | 263 | 60% helix, 13% strand | P32322 |
| B, D | Pyrroline-5-carboxylate reductase 1, mitochondrial (EC 1.5.1.2) | protein | 279 | 59% helix, 13% strand | P32322 |
| C | Pyrroline-5-carboxylate reductase 1, mitochondrial (EC 1.5.1.2) | protein | 277 | 60% helix, 13% strand | P32322 |
| E | Pyrroline-5-carboxylate reductase 1, mitochondrial (EC 1.5.1.2) | protein | 275 | 60% helix, 13% strand | P32322 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains C, D, E
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 967 | 0.76 | 0.78 | 90 | SO4 |
| 2 | 672 | 0.74 | 0.81 | 82 | NDP, SO4 |
| 3 | 61 | 0.74 | 0.99 | 19 | empty |
| 4 | 521 | 0.71 | 0.80 | 60 | SO4 |
| 5 | 308 | 0.66 | 0.81 | 53 | SO4 |
Interfaces
8 interfaces between chains.
- C–D · 4442 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 4366 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 617 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 410 Ų buried · 5 hydrogen bonds · protein-protein
- C–E · 403 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5UAT · Structure of human PYCR-1 complexed with NADPH · the same entry in another collection · chain E against E, TM-score 1.00
- P32322 · AlphaFold monomer V2.0 prediction for pyrroline-5-carboxylate reductase 1, mitochondrial… · a predicted model of the same protein · chain A against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P32322
- Elsewhere: RCSB PDB 5UAT · PDBe 5UAT · UniProt P32322
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.