MolNFT v1 · #135833 · protein
Structure of human pycr-1 complexed with proline
5UAU · Pyrroline-5-carboxylate reductase 1, mitochondrial: “Structure of human pycr-1 complexed with proline”. X-ray diffraction, 2 ligands (PRO, SO4), 13 pockets (best druggability 0.77). MolNFT v1 #135833 on GenesisL1: 3D structure…
- PDB
- 5UAU
- Type
- protein
- Length
- 1,365 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
- PRO, SO4
- Pockets
- 13 · best druggability 0.77
Structure
x-ray diffraction · 5 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 | 274 | 60% helix, 13% strand | P32322 |
| B | Pyrroline-5-carboxylate reductase 1, mitochondrial (EC 1.5.1.2) | protein | 277 | 60% helix, 13% strand | P32322 |
| C | Pyrroline-5-carboxylate reductase 1, mitochondrial (EC 1.5.1.2) | protein | 272 | 60% helix, 13% strand | P32322 |
| D | Pyrroline-5-carboxylate reductase 1, mitochondrial (EC 1.5.1.2) | protein | 275 | 61% helix, 13% strand | P32322 |
| E | Pyrroline-5-carboxylate reductase 1, mitochondrial (EC 1.5.1.2) | protein | 267 | 58% helix, 13% strand | P32322 |
Ligands and binding sites
- PRO · Proline · ligand · 10 copies · chains A, B, C, D, E
- SO4 · Sulfate ion · ion · 4 copies · chains B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 78 | 0.77 | 0.99 | 24 | empty |
| 2 | 68 | 0.75 | 0.99 | 20 | empty |
| 3 | 747 | 0.73 | 0.79 | 73 | PRO, SO4 |
| 4 | 530 | 0.71 | 0.80 | 50 | PRO, SO4 |
| 5 | 580 | 0.70 | 0.79 | 71 | SO4, PRO |
Interfaces
8 interfaces between chains.
- C–D · 4426 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 4411 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 600 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 400 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 391 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5UAU · Structure of human PYCR-1 complexed with proline · the same entry in another collection · chain D against D, 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 D against A, TM-score 1.00
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 5UAU · PDBe 5UAU · UniProt P32322
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