Research workbench
Plp-dependent L-arginine hydroxylase rohp quinonoid I complex
Analyse Plp-dependent L-arginine hydroxylase rohp quinonoid I complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6C3C
- Type
- protein
- Length
- 731 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein
- Ligands
- EJ1
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein | protein | 365 | 50% helix, 15% strand | — |
| B | Uncharacterized protein | protein | 366 | 51% helix, 15% strand | — |
Ligands and binding sites
- EJ1 · (2E)-5-carbamimidamido-2-{[(Z)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4(1H)-ylidene}methyl]imino}pentanoic acid · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 302 | 0.76 | 0.87 | 34 | EDO, EJ1 |
| 2 | 279 | 0.74 | 0.87 | 34 | EDO, EJ1 |
| 3 | 54 | 0.73 | 0.99 | 14 | empty |
| 4 | 191 | 0.55 | 0.79 | 27 | empty |
| 5 | 205 | 0.53 | 0.78 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 2100 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 6C3C · PLP-dependent L-arginine hydroxylase RohP quinonoid I complex · the same entry in another collection · chain B against B, 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 6C3C · PDBe 6C3C
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