Research workbench
Structure of prokaryotic transcription factors
Analyse Structure of prokaryotic transcription factors in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NBC
- Type
- protein
- Length
- 510 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferric uptake regulation protein
- UniProt
- A0A0E2ZLC3
- Ligands
- MN, ZN
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ferric uptake regulation protein | protein | 131 | 37% helix, 24% strand | A0A0E2ZLC3 |
| B | Ferric uptake regulation protein | protein | 130 | 38% helix, 25% strand | A0A0E2ZLC3 |
| C | Ferric uptake regulation protein | protein | 125 | 39% helix, 22% strand | A0A0E2ZLC3 |
| D | Ferric uptake regulation protein | protein | 124 | 40% helix, 23% strand | A0A0E2ZLC3 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 873 | 0.85 | 0.87 | 94 | empty |
| 2 | 138 | 0.64 | 0.87 | 23 | empty |
| 3 | 169 | 0.64 | 0.85 | 32 | empty |
| 4 | 156 | 0.63 | 0.86 | 23 | empty |
| 5 | 208 | 0.57 | 0.79 | 38 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1550 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 1486 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 768 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 652 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 217 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5NBC · Structure of Prokaryotic Transcription Factors · 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 A0A0E2ZLC3
- Elsewhere: RCSB PDB 5NBC · PDBe 5NBC · UniProt A0A0E2ZLC3
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