MolNFT v1 · #169851 · protein
Structure of human PYCR1 complexed with N-formyl L-proline
6XP0 · Pyrroline-5-carboxylate reductase 1, mitochondrial: “Structure of human PYCR1 complexed with N-formyl L-proline”. X-ray diffraction, 1 ligand (FPK), 11 pockets (best druggability 0.75). MolNFT v1 #169851 on GenesisL1: 3D structure…
- PDB
- 6XP0
- Type
- protein
- Length
- 1,375 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
- FPK
- Pockets
- 11 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 59% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyrroline-5-carboxylate reductase 1, mitochondrial (EC 1.5.1.2) | protein | 272 | 60% helix, 14% strand | P32322 |
| B | Pyrroline-5-carboxylate reductase 1, mitochondrial (EC 1.5.1.2) | protein | 279 | 58% helix, 13% strand | P32322 |
| C | Pyrroline-5-carboxylate reductase 1, mitochondrial (EC 1.5.1.2) | protein | 275 | 59% helix, 13% strand | P32322 |
| D | Pyrroline-5-carboxylate reductase 1, mitochondrial (EC 1.5.1.2) | protein | 276 | 58% helix, 13% strand | P32322 |
| E | Pyrroline-5-carboxylate reductase 1, mitochondrial (EC 1.5.1.2) | protein | 273 | 59% helix, 14% strand | P32322 |
Ligands and binding sites
- FPK · 1-formyl-L-proline · ligand · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1011 | 0.75 | 0.78 | 85 | FPK |
| 2 | 763 | 0.73 | 0.78 | 86 | FPK |
| 3 | 541 | 0.70 | 0.79 | 54 | FPK |
| 4 | 319 | 0.69 | 0.83 | 34 | FPK |
| 5 | 265 | 0.50 | 0.74 | 27 | empty |
Interfaces
8 interfaces between chains.
- A–B · 4487 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 4460 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 655 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 411 Ų buried · 7 hydrogen bonds · protein-protein
- C–E · 410 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6XP0 · Structure of human PYCR1 complexed with N-formyl L-proline · 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 E 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 6XP0 · PDBe 6XP0 · UniProt P32322
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