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Crystal structure of 1-pyrroline-5-carboxylate dehydrogenase from bacillus licheniformis (target nysgrc-000337)
Analyse Crystal structure of 1-pyrroline-5-carboxylate dehydrogenase from bacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RJL
- Type
- protein
- Length
- 4,105 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 1-pyrroline-5-carboxylate dehydrogenase
- EC
- 1.5.1.12
- UniProt
- Q65NN2
- Ligands
- CD
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, F, G, H | 1-pyrroline-5-carboxylate dehydrogenase (EC 1.5.1.12) | protein | 513 | 40% helix, 23% strand | Q65NN2 |
| B | 1-pyrroline-5-carboxylate dehydrogenase (EC 1.5.1.12) | protein | 514 | 40% helix, 23% strand | Q65NN2 |
Ligands and binding sites
- CD · Cadmium ion · metal · 47 copies · chains A, B, D, C, E, F, H, G
- ACT · Acetate ion · additive · 8 copies · chains A, D, B, E, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1140 | 0.81 | 0.82 | 105 | CD |
| 2 | 1172 | 0.81 | 0.82 | 105 | CD, ACT |
| 3 | 797 | 0.79 | 0.82 | 78 | CD, ACT |
| 4 | 929 | 0.77 | 0.80 | 133 | empty |
| 5 | 669 | 0.75 | 0.81 | 68 | empty |
Interfaces
16 interfaces between chains.
- A–B · 720 Ų buried · 14 hydrogen bonds · protein-protein
- E–F · 709 Ų buried · 18 hydrogen bonds · protein-protein
- E–G · 536 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 528 Ų buried · 5 hydrogen bonds · protein-protein
- B–E · 516 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3RJL · Crystal structure of 1-pyrroline-5-carboxylate dehydrogenase from Bacillus licheniformis… · the same entry in another collection · chain H against H, TM-score 1.00
- Q65NN2 · AlphaFold monomer V2.0 prediction for 1-pyrroline-5-carboxylate dehydrogenase (Q65NN2) · a predicted model of the same protein · chain B 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 Q65NN2
- Elsewhere: RCSB PDB 3RJL · PDBe 3RJL · UniProt Q65NN2
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