Research workbench
The structure of mppp soaked with the products 4HKA and 2KA
Analyse The structure of mppp soaked with the products 4HKA and 2KA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6C9B
- Type
- protein
- Length
- 1,428 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
- EGV, CL
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Plp-dependent L-arginine hydroxylase mppp | protein | 353 | 48% helix, 15% strand | A0A0X1KHF5 |
| B | Plp-dependent L-arginine hydroxylase mppp | protein | 369 | 47% helix, 15% strand | A0A0X1KHF5 |
Ligands and binding sites
- EGV · (4S)-5-carbamimidamido-4-hydroxy-2-oxopentanoic acid · ligand · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 794 | 0.83 | 0.86 | 119 | empty |
| 2 | 319 | 0.73 | 0.86 | 42 | CL |
| 3 | 475 | 0.70 | 0.80 | 60 | CL |
| 4 | 375 | 0.64 | 0.79 | 48 | empty |
| 5 | 307 | 0.60 | 0.78 | 54 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1966 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1584 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 412 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 369 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 232 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (cofactor).
Compared structures
- 6C9B · The structure of MppP soaked with the products 4HKA and 2KA · 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 6C9B · PDBe 6C9B · UniProt A0A0X1KHF5
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