MolNFT v1 · #99395 · protein
Crystal structure of non-heme iron oxygenase orfp in complex with fe, succinate, and (3S)-hydroxy-L-arg
4M26 · L-arginine beta-hydroxylase: “Crystal structure of non-heme iron oxygenase orfp in complex with fe, succinate, and (3S)-hydroxy-L-arg”. X-ray diffraction, 3 ligands (AKG, ZZU, FE), 10 pockets (best druggability 0.81). MolNFT v1…
- PDB
- 4M26
- Type
- protein
- Length
- 1,318 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-arginine beta-hydroxylase
- UniProt
- G9MBV2
- Ligands
- AKG, ZZU, FE
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | L-arginine beta-hydroxylase | protein | 336 | 36% helix, 22% strand | G9MBV2 |
| B | L-arginine beta-hydroxylase | protein | 314 | 32% helix, 22% strand | G9MBV2 |
| C | L-arginine beta-hydroxylase | protein | 332 | 33% helix, 22% strand | G9MBV2 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 2 copies · chains A, B
- ZZU · (2S,3S)-3-hydroxyarginine · ligand · 2 copies · chains C, D
- FE · Fe (III) ion · metal · 5 copies · chains A, B, C, D
- SIN · Succinic acid · additive · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 214 | 0.81 | 0.95 | 37 | SIN, ZZU |
| 2 | 186 | 0.80 | 0.95 | 36 | SIN, ZZU |
| 3 | 548 | 0.79 | 0.86 | 91 | empty |
| 4 | 466 | 0.79 | 0.87 | 86 | empty |
| 5 | 449 | 0.77 | 0.85 | 44 | FE, AKG |
Interfaces
4 interfaces between chains.
- A–B · 1601 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 1549 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 451 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 42 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4M26 · Crystal structure of non-heme iron oxygenase OrfP in complex with Fe, succinate, and… · the same entry in another collection · chain C against C, 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 G9MBV2
- Elsewhere: RCSB PDB 4M26 · PDBe 4M26 · UniProt G9MBV2
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