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Crystal structure of proline utilization a (puta) from geobacter sulfurreducens pca inactivated by N-propargylglycine
Analyse Crystal structure of proline utilization a (puta) from geobacter sulfurreducens… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NME
- Type
- protein
- Length
- 1,950 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proline dehydrogenase and delta-1-pyrroline-5-carboxylate dehydrogenase
- EC
- 1.5.99.8, 1.5.1.12, 1.2.1.88
- UniProt
- Q746X3
- Ligands
- P5F
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Proline dehydrogenase and delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.5.99.8, 1.5.1.12, 1.2.1.88) | protein | 972 | 48% helix, 17% strand | Q746X3 |
| B | Proline dehydrogenase and delta-1-pyrroline-5-carboxylate dehydrogenase (EC 1.5.99.8, 1.5.1.12, 1.2.1.88) | protein | 978 | 49% helix, 17% strand | Q746X3 |
Ligands and binding sites
- P5F · N-propargylglycine-modified flavin adenine dinucleotide · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 16 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 707 | 0.86 | 0.90 | 72 | P5F |
| 2 | 603 | 0.84 | 0.89 | 69 | P5F |
| 3 | 485 | 0.84 | 0.91 | 81 | EDO |
| 4 | 446 | 0.83 | 0.91 | 85 | EDO |
| 5 | 672 | 0.79 | 0.84 | 80 | EDO |
Interfaces
1 interface between chains.
- A–B · 4428 Ų buried · 81 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4NME · Crystal structure of proline utilization A (PutA) from Geobacter sulfurreducens PCA… · 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 Q746X3
- Elsewhere: RCSB PDB 4NME · PDBe 4NME · UniProt Q746X3
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