MolNFT v2 · #220857 · protein
Structure of PYCR1 complexed with 5-oxo-7a-phenyl-hexahydropyrrolo[2,1-b][1,3]thiazole-3-carboxylic acid
8TD0 · Pyrroline-5-carboxylate reductase 1, mitochondrial: “Structure of PYCR1 complexed with 5-oxo-7a-phenyl-hexahydropyrrolo[2,1-b][1,3]thiazole-3-carboxylic acid”. X-ray diffraction at 2.2, 2 ligands (ZS5, SO4), 12 pockets (best…
- PDB
- 8TD0
- Type
- protein
- Length
- 1,385 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.2
- Source
- Homo sapiens
- Molecule
- Pyrroline-5-carboxylate reductase 1, mitochondrial
- EC
- 1.5.1.2
- UniProt
- P32322
- Ligands
- ZS5, SO4
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · resolution 2.2 · 4 distinct chains · 58% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyrroline-5-carboxylate reductase 1, mitochondrial (EC 1.5.1.2) | protein | 280 | 59% helix, 13% strand | P32322 |
| B | Pyrroline-5-carboxylate reductase 1, mitochondrial (EC 1.5.1.2) | protein | 279 | 57% helix, 13% strand | P32322 |
| C, E | Pyrroline-5-carboxylate reductase 1, mitochondrial (EC 1.5.1.2) | protein | 274 | 57% helix, 14% strand | P32322 |
| D | Pyrroline-5-carboxylate reductase 1, mitochondrial (EC 1.5.1.2) | protein | 278 | 58% helix, 13% strand | P32322 |
Ligands and binding sites
- ZS5 · (3R,4S,7aR)-5-oxo-7a-phenylhexahydropyrrolo[2,1-b][1,3]thiazole-3-carboxylic acid · ligand · 2 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, D, B, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1003 | 0.77 | 0.79 | 86 | SO4, ZS5 |
| 2 | 726 | 0.74 | 0.79 | 69 | ZS5 |
| 3 | 516 | 0.71 | 0.80 | 53 | SO4 |
| 4 | 385 | 0.70 | 0.82 | 53 | SO4 |
| 5 | 275 | 0.51 | 0.74 | 40 | empty |
Interfaces
8 interfaces between chains.
- C–D · 4411 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 4409 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 620 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 398 Ų buried · 5 hydrogen bonds · protein-protein
- A–E · 397 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- P32322 · AlphaFold monomer V2.0 prediction for pyrroline-5-carboxylate reductase 1, mitochondrial… · a predicted model of the same protein · chain C 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 8TD0 · PDBe 8TD0 · UniProt P32322
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