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Crystal structure of proline utilization a (puta) from geobacter sulfurreducens pca inactivated by N-propargylglycine and complexed with menadione bisulfite
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
- 4NMF
- Type
- protein
- Length
- 1,952 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, 2L3, 2LB
- 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 | 973 | 49% 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 | 979 | 49% helix, 17% strand | Q746X3 |
Ligands and binding sites
- P5F · N-propargylglycine-modified flavin adenine dinucleotide · ligand · 2 copies · chains A, B
- 2L3 · (2R)-2-methyl-1,4-dioxo-1,2,3,4-tetrahydronaphthalene-2-sulfonic acid · ligand · 2 copies · chains A, B
- 2LB · (2S)-2-methyl-1,4-dioxo-1,2,3,4-tetrahydronaphthalene-2-sulfonic acid · ligand · chains B
- EDO · 1,2-ethanediol · additive · 8 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 | 692 | 0.86 | 0.90 | 74 | P5F, 2L3, 2LB |
| 2 | 489 | 0.84 | 0.90 | 86 | empty |
| 3 | 357 | 0.83 | 0.92 | 50 | P5F, 2L3 |
| 4 | 287 | 0.82 | 0.93 | 61 | EDO |
| 5 | 720 | 0.79 | 0.83 | 76 | EDO |
Interfaces
1 interface between chains.
- A–B · 4532 Ų buried · 71 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4NMF · 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 4NMF · PDBe 4NMF · UniProt Q746X3
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