MolNFT v1 · #105651 · protein + DNA
Crystal structure of magnetospirillum gryphiswaldense msr-1 semet-fur- MN2+-FEOAB1 operator
4RB2 · DNA (25-mer): “Crystal structure of magnetospirillum gryphiswaldense msr-1 semet-fur- MN2+-FEOAB1 operator”. X-ray diffraction, 1 ligand (MN), 5 pockets (best druggability 0.65). MolNFT v1 #105651 on GenesisL1: 3D structure, binding…
- PDB
- 4RB2
- Type
- protein + DNA
- Length
- 318 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (25-mer); DNA-binding transcriptional dual regulator of siderophore biosynthesis and…
- UniProt
- V6F4Q0
- Ligands
- MN
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (25-mer) | dna | 25 | — | — |
| B | DNA (25-mer) | dna | 25 | — | — |
| C | DNA-binding transcriptional dual regulator of siderophore biosynthesis and TRANSPORT(FUR family) | protein | 134 | 43% helix, 24% strand | V6F4Q0 |
| D | DNA-binding transcriptional dual regulator of siderophore biosynthesis and TRANSPORT(FUR family) | protein | 134 | 42% helix, 24% strand | V6F4Q0 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 663 | 0.65 | 0.75 | 60 | empty |
| 2 | 95 | 0.44 | 0.80 | 17 | empty |
| 3 | 102 | 0.39 | 0.76 | 17 | empty |
| 4 | 95 | 0.38 | 0.76 | 15 | empty |
| 5 | 87 | 0.35 | 0.75 | 14 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1435 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1072 Ų buried · 106 hydrogen bonds · nucleic-nucleic
- B–D · 547 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–C · 412 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–D · 409 Ų buried · 11 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 4RB2 · Crystal structure of Magnetospirillum gryphiswaldense MSR-1 SeMet-Fur-Mn2+-feoAB1 operator · 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 4RB2 · PDBe 4RB2 · UniProt V6F4Q0
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