MolNFT v1 · #169852 · protein
Structure of human PYCR1 complexed with L-thiazolidine-2-carboxylate
6XP1 · Pyrroline-5-carboxylate reductase 1, mitochondrial: “Structure of human PYCR1 complexed with L-thiazolidine-2-carboxylate”. X-ray diffraction, 2 ligands (T2C, SO4), 15 pockets (best druggability 0.76). MolNFT v1 #169852 on…
- PDB
- 6XP1
- Type
- protein
- Length
- 1,378 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
- T2C, SO4
- Pockets
- 15 · 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 | 266 | 61% helix, 13% strand | P32322 |
| B, D | Pyrroline-5-carboxylate reductase 1, mitochondrial (EC 1.5.1.2) | protein | 281 | 59% helix, 13% strand | P32322 |
| C | Pyrroline-5-carboxylate reductase 1, mitochondrial (EC 1.5.1.2) | protein | 274 | 60% helix, 14% strand | P32322 |
| E | Pyrroline-5-carboxylate reductase 1, mitochondrial (EC 1.5.1.2) | protein | 276 | 61% helix, 13% strand | P32322 |
Ligands and binding sites
- T2C · (2S)-1,3-thiazolidine-2-carboxylic acid · ligand · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1061 | 0.76 | 0.78 | 90 | T2C |
| 2 | 66 | 0.75 | 0.99 | 20 | empty |
| 3 | 869 | 0.75 | 0.78 | 98 | SO4 |
| 4 | 59 | 0.73 | 0.98 | 20 | empty |
| 5 | 497 | 0.71 | 0.81 | 48 | SO4 |
Interfaces
8 interfaces between chains.
- A–B · 4482 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 4436 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 606 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 407 Ų buried · 7 hydrogen bonds · protein-protein
- C–E · 394 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6XP1 · Structure of human PYCR1 complexed with L-thiazolidine-2-carboxylate · 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 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 6XP1 · PDBe 6XP1 · UniProt P32322
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