MolNFT v1 · #99403 · protein
Crystal structure of non-heme iron oxygenase orfp in complex with fe and L-canavanine
4M2F · L-arginine beta-hydroxylase: “Crystal structure of non-heme iron oxygenase orfp in complex with fe and L-canavanine”. X-ray diffraction, 2 ligands (GGB, FE), 12 pockets (best druggability 0.80). MolNFT v1 #99403 on GenesisL1: 3D…
- PDB
- 4M2F
- Type
- protein
- Length
- 1,321 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-arginine beta-hydroxylase
- UniProt
- G9MBV2
- Ligands
- GGB, FE
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | L-arginine beta-hydroxylase | protein | 336 | 37% helix, 21% strand | G9MBV2 |
| B | L-arginine beta-hydroxylase | protein | 313 | 32% helix, 20% strand | G9MBV2 |
Ligands and binding sites
- GGB · L-canavanine · ligand · 2 copies · chains C, D
- FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 395 | 0.80 | 0.89 | 71 | empty |
| 2 | 582 | 0.80 | 0.86 | 95 | empty |
| 3 | 173 | 0.80 | 0.95 | 38 | FE, GGB |
| 4 | 152 | 0.79 | 0.96 | 38 | GGB |
| 5 | 1037 | 0.77 | 0.79 | 83 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1578 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 1542 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 455 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 38 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4M2F · Crystal structure of non-heme iron oxygenase OrfP in complex with Fe and L-canavanine · 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 4M2F · PDBe 4M2F · UniProt G9MBV2
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