Research workbench
Crystal structure of non-heme iron oxygenase orfp in complex with fe and D-arg
Analyse Crystal structure of non-heme iron oxygenase orfp in complex with fe and D-arg in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4M2C
- Type
- protein
- Length
- 1,327 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-arginine beta-hydroxylase
- UniProt
- G9MBV2
- Ligands
- DAR, FE
- Pockets
- 15 · best druggability 0.83
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 | 34% helix, 21% strand | G9MBV2 |
| B | L-arginine beta-hydroxylase | protein | 319 | 34% helix, 20% strand | G9MBV2 |
Ligands and binding sites
- DAR · D-arginine · ligand · 2 copies · chains C, D
- FE · Fe (III) ion · metal · 3 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 293 | 0.83 | 0.94 | 54 | empty |
| 2 | 157 | 0.80 | 0.96 | 31 | FE, DAR |
| 3 | 411 | 0.79 | 0.88 | 73 | empty |
| 4 | 155 | 0.79 | 0.95 | 34 | FE, DAR |
| 5 | 885 | 0.74 | 0.77 | 66 | FE |
Interfaces
4 interfaces between chains.
- A–B · 1675 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 1534 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 468 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 136 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4M2C · Crystal structure of non-heme iron oxygenase OrfP in complex with Fe and D-Arg · 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 4M2C · PDBe 4M2C · UniProt G9MBV2
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