Research workbench
Crystal structure of P5CR complexed with NADH
Analyse Crystal structure of P5CR complexed with NADH in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GR9
- Type
- protein
- Length
- 1,384 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
- NAI, GLU
- Pockets
- 19 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E | Pyrroline-5-carboxylate reductase 1 (EC 1.5.1.2) | protein | 277 | 53% helix, 13% strand | P32322 |
| B | Pyrroline-5-carboxylate reductase 1 (EC 1.5.1.2) | protein | 276 | 45% helix, 6% strand | P32322 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 5 copies · chains A, B, C, D, E
- GLU · Glutamic acid · ligand · 5 copies · chains B, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 523 | 0.59 | 0.73 | 56 | empty |
| 2 | 414 | 0.56 | 0.73 | 45 | empty |
| 3 | 389 | 0.56 | 0.74 | 43 | empty |
| 4 | 392 | 0.54 | 0.73 | 40 | empty |
| 5 | 248 | 0.50 | 0.75 | 37 | empty |
Interfaces
5 interfaces between chains.
- B–E · 398 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 392 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 388 Ų buried · 5 hydrogen bonds · protein-protein
- A–E · 375 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 370 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
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 2GR9 · PDBe 2GR9 · UniProt P32322
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