MolNFT v1 · #105650 · protein + DNA
Crystal structure of magnetospirillum gryphiswaldense msr-1 fur-MN2+- E. COLI fur box
4RB1 · DNA-binding transcriptional dual regulator of siderophore…: “Crystal structure of magnetospirillum gryphiswaldense msr-1 fur-MN2+- E. COLI fur box”. X-ray diffraction, 1 ligand (MN), 6 pockets (best druggability 0.48). MolNFT v1…
- PDB
- 4RB1
- Type
- protein + DNA
- Length
- 288 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-binding transcriptional dual regulator of siderophore biosynthesis and TRANSPORT(FUR…
- UniProt
- V6F4Q0
- Ligands
- MN
- Pockets
- 6 · best druggability 0.48
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-binding transcriptional dual regulator of siderophore biosynthesis and TRANSPORT(FUR family) | protein | 132 | 42% helix, 20% strand | V6F4Q0 |
| B | DNA-binding transcriptional dual regulator of siderophore biosynthesis and TRANSPORT(FUR family) | protein | 132 | 41% helix, 21% strand | V6F4Q0 |
| D | DNA (5'- D(*CP*GP*CP*GP*AP*TP*AP*AP*TP*GP*AP*TP*AP*AP*TP*CP*AP*TP*TP*AP*TP*CP* CP*GP*C)-3') | dna | 24 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 216 | 0.48 | 0.75 | 28 | empty |
| 2 | 79 | 0.41 | 0.80 | 17 | empty |
| 3 | 59 | 0.38 | 0.80 | 19 | empty |
| 4 | 129 | 0.38 | 0.74 | 14 | empty |
| 5 | 95 | 0.31 | 0.73 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1117 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 467 Ų buried · 6 hydrogen bonds · protein-nucleic
- B–D · 330 Ų buried · 10 hydrogen bonds · protein-nucleic
Compared structures
- 4RB1 · Crystal structure of Magnetospirillum gryphiswaldense MSR-1 Fur-Mn2+-E. coli Fur box · 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 V6F4Q0
- Elsewhere: RCSB PDB 4RB1 · PDBe 4RB1 · UniProt V6F4Q0
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