Research workbench
Structure of the plp-dependent L-arginine hydroxylase mppp with D- arginine bound
Analyse Structure of the plp-dependent L-arginine hydroxylase mppp with D- arginine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DJ3
- Type
- protein
- Length
- 1,404 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plp-dependent L-arginine hydroxylase mppp
- Ligands
- 5DK, MG
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Plp-dependent L-arginine hydroxylase mppp | protein | 351 | 48% helix, 16% strand | — |
Ligands and binding sites
- 5DK · (E)-N~2~-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-D-arginine · ligand · 4 copies · chains A, C, B, D
- MG · Magnesium ion · metal · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 922 | 0.79 | 0.82 | 117 | 5DK, MG |
| 2 | 397 | 0.73 | 0.84 | 59 | 5DK |
| 3 | 546 | 0.73 | 0.81 | 70 | 5DK |
| 4 | 478 | 0.72 | 0.82 | 60 | 5DK |
| 5 | 521 | 0.70 | 0.80 | 59 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1583 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 1582 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 456 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 327 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 140 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5DJ3 · Structure of the PLP-Dependent L-Arginine Hydroxylase MppP with D-Arginine Bound · 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 5DJ3 · PDBe 5DJ3
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