MolNFT v1 · #146212 · protein
X-ray crystal structure of napi L-arginine desaturase bound to FE(II), L-arginine, and acetate
6DAW · Non-heme iron hydroxylase: “X-ray crystal structure of napi L-arginine desaturase bound to FE(II), L-arginine, and acetate”. X-ray diffraction, 2 ligands (ARG, FE2), 10 pockets (best druggability 0.80). MolNFT v1 #146212 on…
- PDB
- 6DAW
- Type
- protein
- Length
- 683 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-heme iron hydroxylase
- EC
- 1.14.-.-
- UniProt
- S4TL40
- Ligands
- ARG, FE2
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Non-heme iron hydroxylase (EC 1.14.-.-) | protein | 342 | 35% helix, 21% strand | S4TL40 |
| B | Non-heme iron hydroxylase (EC 1.14.-.-) | protein | 341 | 35% helix, 21% strand | S4TL40 |
Ligands and binding sites
- ARG · Arginine · ligand · 2 copies · chains A, B
- FE2 · Fe (II) ion · metal · 2 copies · chains A, B
- ACT · Acetate ion · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 173 | 0.80 | 0.96 | 32 | FE2, ARG, ACT |
| 2 | 181 | 0.80 | 0.95 | 36 | FE2, ARG, ACT |
| 3 | 78 | 0.71 | 0.97 | 20 | empty |
| 4 | 109 | 0.67 | 0.91 | 26 | empty |
| 5 | 366 | 0.58 | 0.75 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 1463 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 6DAW · X-ray crystal structure of NapI L-arginine desaturase bound to Fe(II), L-arginine, and… · 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 S4TL40
- Elsewhere: RCSB PDB 6DAW · PDBe 6DAW · UniProt S4TL40
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