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Crystal structure of non-heme iron oxygenase orfp in complex with fe, succinate, and (3R,4R)-dihydroxy-L-arg
Analyse Crystal structure of non-heme iron oxygenase orfp in complex with fe… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4M2G
- Type
- protein
- Length
- 1,312 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-arginine beta-hydroxylase
- UniProt
- G9MBV2
- Ligands
- 2OR, FE
- Pockets
- 16 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | L-arginine beta-hydroxylase | protein | 336 | 36% helix, 20% strand | G9MBV2 |
| B | L-arginine beta-hydroxylase | protein | 309 | 31% helix, 21% strand | G9MBV2 |
| C | L-arginine beta-hydroxylase | protein | 331 | 33% helix, 22% strand | G9MBV2 |
Ligands and binding sites
- 2OR · amino{[(2R,3R,4S)-4-amino-2,3,5-trihydroxy-5-oxopentyl]amino}methaniminium · ligand · 2 copies · chains C, D
- FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
- SIN · Succinic acid · additive · 4 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 277 | 0.83 | 0.94 | 53 | empty |
| 2 | 198 | 0.81 | 0.95 | 36 | FE, 2OR, SIN |
| 3 | 199 | 0.81 | 0.95 | 33 | FE, 2OR, SIN |
| 4 | 358 | 0.80 | 0.90 | 66 | empty |
| 5 | 918 | 0.74 | 0.77 | 90 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1688 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 1570 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 447 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 48 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4M2G · Crystal structure of non-heme iron oxygenase OrfP in complex with Fe, succinate, and… · 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 4M2G · PDBe 4M2G · UniProt G9MBV2
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