MolNFT v2 · #63975 · protein
Crystal Structure of HbpS
3FPV · Extracellular haem-binding protein: “Crystal Structure of HbpS”. X-ray diffraction at 2.2, 1 ligand (FE), 20 pockets (best druggability 0.74). MolNFT v2 #63975 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3FPV
- Type
- protein
- Length
- 1,128 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.2
- Source
- Streptomyces reticuli
- Molecule
- Extracellular haem-binding protein
- UniProt
- Q9RIM2
- Ligands
- FE
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · resolution 2.2 · 1 distinct chain · 43% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Extracellular haem-binding protein | protein | 141 | 43% helix, 25% strand | Q9RIM2 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 8 copies · chains A, G, B, F, C, D, E, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 415 | 0.74 | 0.84 | 49 | empty |
| 2 | 202 | 0.66 | 0.85 | 28 | empty |
| 3 | 214 | 0.65 | 0.84 | 28 | empty |
| 4 | 302 | 0.65 | 0.81 | 41 | empty |
| 5 | 273 | 0.65 | 0.82 | 40 | empty |
Interfaces
17 interfaces between chains.
- A–F · 1262 Ų buried · 35 hydrogen bonds · protein-protein
- C–H · 1238 Ų buried · 33 hydrogen bonds · protein-protein
- B–G · 1223 Ų buried · 37 hydrogen bonds · protein-protein
- D–E · 1185 Ų buried · 31 hydrogen bonds · protein-protein
- F–H · 770 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3FPV · Crystal structure of hbps · 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 Q9RIM2
- Elsewhere: RCSB PDB 3FPV · PDBe 3FPV · UniProt Q9RIM2
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