Research workbench
Structure of the PLP-Dependent L-Arginine Hydroxylase MppP Holoenzyme
Analyse Structure of the PLP-Dependent L-Arginine Hydroxylase MppP Holoenzyme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DJ1
- Type
- protein
- Length
- 1,421 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.102
- Source
- Streptomyces wadayamensis
- Molecule
- PLP-Dependent L-Arginine Hydroxylase MppP
- Ligands
- MG, CL
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · resolution 2.102 · 3 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | PLP-Dependent L-Arginine Hydroxylase MppP | protein | 351 | 48% helix, 15% strand | — |
| B, C | PLP-Dependent L-Arginine Hydroxylase MppP | protein | 353 | 48% helix, 16% strand | — |
| D | PLP-Dependent L-Arginine Hydroxylase MppP | protein | 364 | 49% helix, 15% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1135 | 0.81 | 0.82 | 124 | empty |
| 2 | 536 | 0.66 | 0.77 | 64 | CL |
| 3 | 350 | 0.63 | 0.79 | 29 | empty |
| 4 | 276 | 0.54 | 0.76 | 31 | empty |
| 5 | 138 | 0.49 | 0.79 | 24 | CL |
Interfaces
6 interfaces between chains.
- C–D · 1645 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1605 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 381 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 364 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 260 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (cofactor).
Compared structures
- 5DJ1 · Structure of the plp-dependent L-arginine hydroxylase mppp holoenzyme · 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
- Elsewhere: RCSB PDB 5DJ1 · PDBe 5DJ1
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