Research workbench
The structure of mppp soaked with the substrate L-arg
Analyse The structure of mppp soaked with the substrate L-arg in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6C8T
- Type
- protein
- Length
- 1,458 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Plp-dependent L-arginine hydroxylase mppp
- UniProt
- A0A0X1KHF5
- Ligands
- EQJ, CL
- Pockets
- 17 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Plp-dependent L-arginine hydroxylase mppp | protein | 368 | 49% helix, 15% strand | A0A0X1KHF5 |
| D | Plp-dependent L-arginine hydroxylase mppp | protein | 354 | 48% helix, 15% strand | A0A0X1KHF5 |
Ligands and binding sites
- EQJ · (E)-N~2~-({3-hydroxy-2-methyl-5-[(phosphonooxy) methyl]pyridin-4-yl}methylidene)-L-arginine · ligand · 3 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 145 | 0.80 | 0.97 | 31 | EQJ |
| 2 | 129 | 0.80 | 0.98 | 29 | EQJ |
| 3 | 147 | 0.79 | 0.96 | 32 | EQJ |
| 4 | 683 | 0.76 | 0.81 | 75 | empty |
| 5 | 347 | 0.74 | 0.86 | 46 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2250 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 1932 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 468 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 372 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 217 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (cofactor).
Compared structures
- 6C8T · The structure of MppP soaked with the substrate L-Arg · 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 A0A0X1KHF5
- Elsewhere: RCSB PDB 6C8T · PDBe 6C8T · UniProt A0A0X1KHF5
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