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Crystal structure of non-heme iron oxygenase orfp D157A mutant in complex with (3S)-hydroxy-L-arg
Analyse Crystal structure of non-heme iron oxygenase orfp D157A mutant in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NE0
- Type
- protein
- Length
- 1,279 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-arginine beta-hydroxylase
- UniProt
- G9MBV2
- Ligands
- ZZU, FE
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-arginine beta-hydroxylase | protein | 337 | 36% helix, 21% strand | G9MBV2 |
| B | L-arginine beta-hydroxylase | protein | 304 | 33% helix, 21% strand | G9MBV2 |
| C | L-arginine beta-hydroxylase | protein | 322 | 33% helix, 20% strand | G9MBV2 |
| D | L-arginine beta-hydroxylase | protein | 316 | 32% helix, 22% strand | G9MBV2 |
Ligands and binding sites
- ZZU · (2S,3S)-3-hydroxyarginine · ligand · 2 copies · chains C, D
- FE · Fe (III) ion · metal · 4 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
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 281 | 0.83 | 0.94 | 54 | empty |
| 2 | 409 | 0.81 | 0.89 | 72 | empty |
| 3 | 261 | 0.74 | 0.88 | 35 | FE, SIN, ZZU |
| 4 | 219 | 0.74 | 0.89 | 34 | FE, SIN, ZZU |
| 5 | 434 | 0.73 | 0.83 | 43 | FE |
Interfaces
4 interfaces between chains.
- A–B · 1596 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 1559 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 439 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 34 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4NE0 · Crystal structure of non-heme iron oxygenase OrfP D157A mutant in complex with… · 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 4NE0 · PDBe 4NE0 · UniProt G9MBV2
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