Research workbench
Metal nanoclusters bound to the ferric binding protein from neisseria gonorrhoeae.
Analyse Metal nanoclusters bound to the ferric binding protein from neisseria… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1O7T
- Type
- protein
- Length
- 2,781 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Iron binding protein
- UniProt
- Q50964
- Ligands
- HF5, PHF, HF3
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I | Iron binding protein | protein | 309 | 48% helix, 17% strand | Q50964 |
Ligands and binding sites
- HF5 · Hf oxo cluster HF5 · ligand · 5 copies · chains A, B, C, E, F
- PHF · Hf-oxo-phosphate cluster phf · ligand · 3 copies · chains G, H, I
- HF3 · Smallest hf-oxo-phosphate cluster HF3 · ligand · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 581 | 0.70 | 0.79 | 73 | PHF |
| 2 | 548 | 0.70 | 0.79 | 72 | HF5 |
| 3 | 549 | 0.69 | 0.79 | 83 | PHF |
| 4 | 621 | 0.68 | 0.77 | 49 | empty |
| 5 | 512 | 0.68 | 0.79 | 65 | PHF |
Interfaces
12 interfaces between chains.
- A–I · 364 Ų buried · 3 hydrogen bonds · protein-protein
- F–I · 354 Ų buried · 3 hydrogen bonds · protein-protein
- B–G · 315 Ų buried · 3 hydrogen bonds · protein-protein
- A–H · 305 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 192 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1O7T · Metal nanoclusters bound to the Ferric Binding Protein from Neisseria gonorrhoeae. · the same entry in another collection · chain E against E, 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 Q50964
- Elsewhere: RCSB PDB 1O7T · PDBe 1O7T · UniProt Q50964
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