Research workbench
Crystal structure of human pyrroline-5-carboxylate reductase
Analyse Crystal structure of human pyrroline-5-carboxylate reductase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2IZZ
- 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
- EC
- 1.5.1.2
- UniProt
- P32322
- Ligands
- NAD
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 60% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyrroline-5-carboxylate reductase 1 (EC 1.5.1.2) | protein | 272 | 60% helix, 14% strand | P32322 |
| B | Pyrroline-5-carboxylate reductase 1 (EC 1.5.1.2) | protein | 279 | 59% helix, 13% strand | P32322 |
| C | Pyrroline-5-carboxylate reductase 1 (EC 1.5.1.2) | protein | 276 | 61% helix, 13% strand | P32322 |
| D | Pyrroline-5-carboxylate reductase 1 (EC 1.5.1.2) | protein | 276 | 59% helix, 13% strand | P32322 |
| E | Pyrroline-5-carboxylate reductase 1 (EC 1.5.1.2) | protein | 272 | 60% helix, 14% strand | P32322 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 5 copies · chains A, B, C, D, E
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B, C, 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 | 915 | 0.77 | 0.80 | 79 | NAD, EDO |
| 2 | 867 | 0.75 | 0.79 | 79 | EDO, NAD |
| 3 | 594 | 0.75 | 0.81 | 61 | EDO, NAD |
| 4 | 421 | 0.74 | 0.84 | 50 | NAD, EDO |
| 5 | 54 | 0.74 | 0.99 | 20 | empty |
Interfaces
8 interfaces between chains.
- A–B · 4562 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 4491 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 594 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 402 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 396 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2IZZ · Crystal structure of human pyrroline-5-carboxylate reductase · 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 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 2IZZ · PDBe 2IZZ · UniProt P32322
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