MolNFT v1 · #99831 · protein
Crystal structure of holo-phus, a heme-binding protein from pseudomonas aeruginosa
4MF9 · Hemin degrading factor: “Crystal structure of holo-phus, a heme-binding protein from pseudomonas aeruginosa”. X-ray diffraction, 1 ligand (HEM), 4 pockets (best druggability 0.82). MolNFT v1 #99831 on GenesisL1: 3D structure…
- PDB
- 4MF9
- Type
- protein
- Length
- 687 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemin degrading factor
- UniProt
- O68880
- Ligands
- HEM
- Pockets
- 4 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemin degrading factor | protein | 346 | 31% helix, 33% strand | O68880 |
| B | Hemin degrading factor | protein | 341 | 30% helix, 33% strand | O68880 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 876 | 0.82 | 0.84 | 75 | empty |
| 2 | 776 | 0.80 | 0.83 | 71 | empty |
| 3 | 258 | 0.64 | 0.82 | 39 | HEM |
| 4 | 370 | 0.64 | 0.78 | 40 | HEM |
Interfaces
1 interface between chains.
- A–B · 1260 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (heme attachment).
Compared structures
- 4MF9 · Crystal structure of holo-PhuS, a heme-binding protein from Pseudomonas aeruginosa · 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 O68880
- Elsewhere: RCSB PDB 4MF9 · PDBe 4MF9 · UniProt O68880
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