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Tri-nuclear oxo-iron clusters in the ferric binding protein from N. gonorrhoeae
Analyse Tri-nuclear oxo-iron clusters in the ferric binding protein from N. gonorrhoeae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1R1N
- Type
- protein
- Length
- 2,781 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferric-iron binding protein
- UniProt
- P17259
- Ligands
- CNB, CN1, CNF
- Pockets
- 20 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I | Ferric-iron binding protein | protein | 309 | 46% helix, 17% strand | P17259 |
Ligands and binding sites
- CNB · Oxo-iron cluster 1 · ligand · 4 copies · chains A, B, D, H
- CN1 · Oxo-iron cluster 2 · ligand · 4 copies · chains C, E, G, I
- CNF · Oxo-iron cluster 3 · ligand · chains F
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 | 522 | 0.69 | 0.79 | 87 | CNB |
| 2 | 486 | 0.69 | 0.79 | 76 | CN1 |
| 3 | 259 | 0.68 | 0.84 | 40 | CNB |
| 4 | 382 | 0.66 | 0.80 | 38 | empty |
| 5 | 407 | 0.66 | 0.79 | 58 | CN1 |
Interfaces
12 interfaces between chains.
- F–I · 350 Ų buried · 1 hydrogen bond · protein-protein
- A–I · 328 Ų buried · 4 hydrogen bonds · protein-protein
- A–H · 317 Ų buried · 3 hydrogen bonds · protein-protein
- B–G · 305 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 202 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1R1N · Tri-nuclear oxo-iron clusters in the ferric binding protein from N. gonorrhoeae · the same entry in another collection · chain I against I, TM-score 1.00
- P17259 · AlphaFold monomer V2.0 prediction for major ferric iron-binding protein (P17259) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P17259
- Elsewhere: RCSB PDB 1R1N · PDBe 1R1N · UniProt P17259
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