Research workbench
Structure of human pycr-1 complexed with NADPH and L-tetrahydrofuroic acid
Analyse Structure of human pycr-1 complexed with NADPH and L-tetrahydrofuroic acid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UAV
- Type
- protein
- Length
- 1,388 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
- NDP, TFB
- Pockets
- 14 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 59% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyrroline-5-carboxylate reductase 1, mitochondrial (EC 1.5.1.2) | protein | 278 | 59% helix, 13% strand | P32322 |
| B, D | 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 | 277 | 58% helix, 14% strand | P32322 |
| E | Pyrroline-5-carboxylate reductase 1, mitochondrial (EC 1.5.1.2) | protein | 275 | 61% helix, 13% strand | P32322 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 5 copies · chains A, B, C, D, E
- TFB · Tetrahydrofuran-2-carboxylic acid · ligand · 5 copies · chains A, B, C, D, E
- PEG · Di(hydroxyethyl)ether · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 671 | 0.75 | 0.81 | 64 | TFB, NDP |
| 2 | 594 | 0.74 | 0.81 | 69 | NDP, TFB |
| 3 | 60 | 0.74 | 0.98 | 21 | empty |
| 4 | 490 | 0.73 | 0.82 | 50 | TFB, NDP |
| 5 | 359 | 0.72 | 0.84 | 53 | NDP, TFB |
Interfaces
8 interfaces between chains.
- A–B · 4540 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 4520 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 638 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 413 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 410 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5UAV · Structure of human PYCR-1 complexed with NADPH and L-tetrahydrofuroic 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 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 5UAV · PDBe 5UAV · UniProt P32322
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