Research workbench
Crystal structure of L-proline dehydrogenase from P.HORIKOSHII
Analyse Crystal structure of L-proline dehydrogenase from P.HORIKOSHII in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Y56
- Type
- protein
- Length
- 858 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein PH1363; Sarcosine oxidase
- EC
- 1.5.99.8
- UniProt
- O59088, Q5R1N3
- Ligands
- FMN, ATP, FAD, FE, SO4, CL
- Pockets
- 6 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical protein PH1363 (EC 1.5.99.8) | protein | 484 | 25% helix, 25% strand | O59088 |
| B | Sarcosine oxidase (EC 1.5.99.8) | protein | 374 | 34% helix, 25% strand | Q5R1N3 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · chains A, B
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- FAD · Flavin-adenine dinucleotide · ligand · chains B
- FE · Fe (III) ion · metal · chains A
- SO4 · Sulfate ion · ion · chains A, B
- CL · Chloride ion · ion · chains B
- CXS · 3-cyclohexyl-1-propylsulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1163 | 0.85 | 0.86 | 113 | ATP, CXS |
| 2 | 1127 | 0.83 | 0.84 | 119 | FMN, CL, FAD |
| 3 | 245 | 0.71 | 0.86 | 47 | empty |
| 4 | 163 | 0.46 | 0.76 | 21 | empty |
| 5 | 88 | 0.37 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1978 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1Y56 · Crystal structure of L-proline dehydrogenase from P.horikoshii · 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 O59088
- Every structure of UniProt Q5R1N3
- Elsewhere: RCSB PDB 1Y56 · PDBe 1Y56 · UniProt O59088 · UniProt Q5R1N3
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