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Crystal structure of non-heme iron oxygenase orfp in complex with fe and alpha-ketoglutaric acid
Analyse Crystal structure of non-heme iron oxygenase orfp in complex with fe and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4M25
- Type
- protein
- Length
- 1,284 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-arginine beta-hydroxylase
- UniProt
- G9MBV2
- Ligands
- AKG, FE
- Pockets
- 16 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-arginine beta-hydroxylase | protein | 336 | 36% helix, 21% strand | G9MBV2 |
| B, C | L-arginine beta-hydroxylase | protein | 317 | 31% helix, 21% strand | G9MBV2 |
| D | L-arginine beta-hydroxylase | protein | 314 | 32% helix, 23% strand | G9MBV2 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 4 copies · chains A, B, C, D
- FE · Fe (III) ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 499 | 0.80 | 0.87 | 91 | empty |
| 2 | 496 | 0.79 | 0.86 | 77 | empty |
| 3 | 357 | 0.78 | 0.88 | 42 | FE, AKG |
| 4 | 464 | 0.76 | 0.84 | 43 | FE, AKG |
| 5 | 350 | 0.76 | 0.86 | 40 | FE, AKG |
Interfaces
4 interfaces between chains.
- C–D · 1583 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1572 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 411 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 11 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4M25 · Crystal structure of non-heme iron oxygenase OrfP in complex with Fe 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 G9MBV2
- Elsewhere: RCSB PDB 4M25 · PDBe 4M25 · UniProt G9MBV2
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