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Crystal structure of the delta-pyrroline-5-carboxylate dehydrogenase from mycobacterium tuberculosis
Analyse Crystal structure of the delta-pyrroline-5-carboxylate dehydrogenase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LEM
- Type
- protein
- Length
- 3,251 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 1-pyrroline-5-carboxylate dehydrogenase
- EC
- 1.5.1.12
- UniProt
- O50443
- Ligands
- B12, MG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 1-pyrroline-5-carboxylate dehydrogenase (EC 1.5.1.12) | protein | 542 | 42% helix, 20% strand | O50443 |
| B | 1-pyrroline-5-carboxylate dehydrogenase (EC 1.5.1.12) | protein | 543 | 42% helix, 21% strand | O50443 |
| C, D | 1-pyrroline-5-carboxylate dehydrogenase (EC 1.5.1.12) | protein | 544 | 42% helix, 21% strand | O50443 |
| E | 1-pyrroline-5-carboxylate dehydrogenase (EC 1.5.1.12) | protein | 540 | 43% helix, 21% strand | O50443 |
| F | 1-pyrroline-5-carboxylate dehydrogenase (EC 1.5.1.12) | protein | 538 | 42% helix, 21% strand | O50443 |
Ligands and binding sites
- B12 · Cobalamin · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 3 copies · chains C, D, F
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 | 901 | 0.83 | 0.84 | 121 | empty |
| 2 | 1173 | 0.80 | 0.81 | 143 | empty |
| 3 | 1149 | 0.80 | 0.81 | 148 | empty |
| 4 | 554 | 0.79 | 0.85 | 65 | empty |
| 5 | 534 | 0.78 | 0.85 | 44 | empty |
Interfaces
12 interfaces between chains.
- C–D · 4722 Ų buried · 90 hydrogen bonds · protein-protein
- A–B · 4580 Ų buried · 84 hydrogen bonds · protein-protein
- E–F · 4533 Ų buried · 85 hydrogen bonds · protein-protein
- A–E · 1783 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 1782 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (artifact).
Compared structures
- 4LEM · Crystal structure of the Delta-pyrroline-5-carboxylate dehydrogenase from Mycobacterium… · the same entry in another collection · chain A 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 O50443
- Elsewhere: RCSB PDB 4LEM · PDBe 4LEM · UniProt O50443
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