MolNFT v1 · #101281 · protein
Crystal structure of proline utilization a (puta) from geobacter sulfurreducens pca reduced with dithionite
4NMD · Proline dehydrogenase and delta-1-pyrroline-5-carboxylate…: “Crystal structure of proline utilization a (puta) from geobacter sulfurreducens pca reduced with dithionite”. X-ray diffraction, 1 ligand (FDA), 20 pockets (best…
- PDB
- 4NMD
- Type
- protein
- Length
- 1,959 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
- FDA
- 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 | 979 | 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 | 980 | 49% helix, 17% strand | Q746X3 |
Ligands and binding sites
- FDA · Dihydroflavine-adenine dinucleotide · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 14 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 598 | 0.86 | 0.91 | 100 | EDO |
| 2 | 677 | 0.86 | 0.90 | 72 | FDA |
| 3 | 587 | 0.85 | 0.91 | 103 | EDO |
| 4 | 577 | 0.84 | 0.89 | 63 | FDA |
| 5 | 880 | 0.80 | 0.82 | 114 | EDO |
Interfaces
1 interface between chains.
- A–B · 4464 Ų buried · 76 hydrogen bonds · protein-protein
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 4NMD · PDBe 4NMD · UniProt Q746X3
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