Research workbench
Structure of human PYCR1 complexed with cyclopentanecarboxylic acid
Analyse Structure of human PYCR1 complexed with cyclopentanecarboxylic acid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XP3
- Type
- protein
- Length
- 1,382 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
- IQ0, SO4
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · 3 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 | 276 | 59% 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, E | Pyrroline-5-carboxylate reductase 1, mitochondrial (EC 1.5.1.2) | protein | 274 | 60% helix, 14% strand | P32322 |
Ligands and binding sites
- IQ0 · cyclopentanecarboxylic acid · ligand · 2 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, D, 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1037 | 0.77 | 0.79 | 97 | IQ0, SO4 |
| 2 | 511 | 0.75 | 0.83 | 57 | SO4 |
| 3 | 787 | 0.74 | 0.79 | 73 | IQ0 |
| 4 | 57 | 0.74 | 0.99 | 21 | empty |
| 5 | 426 | 0.71 | 0.82 | 54 | SO4 |
Interfaces
8 interfaces between chains.
- A–B · 4509 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 4453 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 605 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 397 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 396 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6XP3 · Structure of human PYCR1 complexed with cyclopentanecarboxylic acid · 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 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 6XP3 · PDBe 6XP3 · UniProt P32322
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