MolNFT v1 · #99405 · protein
Crystal structure of non-heme iron oxygenase orfp in complex with fe
4M2I · L-arginine beta-hydroxylase: “Crystal structure of non-heme iron oxygenase orfp in complex with fe”. X-ray diffraction, 1 ligand (FE), 17 pockets (best druggability 0.84). MolNFT v1 #99405 on GenesisL1: 3D structure, binding sites…
- PDB
- 4M2I
- Type
- protein
- Length
- 1,241 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-arginine beta-hydroxylase
- UniProt
- G9MBV2
- Ligands
- FE
- Pockets
- 17 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-arginine beta-hydroxylase | protein | 321 | 32% helix, 22% strand | G9MBV2 |
| B | L-arginine beta-hydroxylase | protein | 299 | 33% helix, 21% strand | G9MBV2 |
| C | L-arginine beta-hydroxylase | protein | 311 | 31% helix, 21% strand | G9MBV2 |
| D | L-arginine beta-hydroxylase | protein | 310 | 34% helix, 21% strand | G9MBV2 |
Ligands and binding sites
- 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
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 263 | 0.84 | 0.96 | 53 | empty |
| 2 | 226 | 0.81 | 0.95 | 45 | empty |
| 3 | 1115 | 0.76 | 0.78 | 72 | empty |
| 4 | 673 | 0.76 | 0.81 | 72 | empty |
| 5 | 460 | 0.72 | 0.82 | 40 | FE |
Interfaces
4 interfaces between chains.
- C–D · 1657 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 1636 Ų buried · 39 hydrogen bonds · protein-protein
- B–C · 484 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 100 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4M2I · Crystal structure of non-heme iron oxygenase OrfP in complex with Fe · 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 4M2I · PDBe 4M2I · UniProt G9MBV2
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