MolNFT v1 · #68285 · protein + DNA
Crystal structure of fis bound to 27 bp DNA F25 containing T2A3 sequence at center
3JRD · DNA-binding protein fis: “Crystal structure of fis bound to 27 bp DNA F25 containing T2A3 sequence at center”. X-ray diffraction, 3 pockets (best druggability 0.61). MolNFT v1 #68285 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3JRD
- Type
- protein + DNA
- Length
- 243 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-binding protein fis; DNA (27-mer)
- UniProt
- P0A6R3
- Pockets
- 3 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 58% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-binding protein fis | protein | 91 | 58% helix, 13% strand | P0A6R3 |
| B | DNA-binding protein fis | protein | 98 | 57% helix, 10% strand | P0A6R3 |
| C | DNA (27-mer) | dna | 27 | — | — |
| D | DNA (27-mer) | dna | 27 | — | — |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 409 | 0.61 | 0.77 | 39 | empty |
| 2 | 154 | 0.45 | 0.76 | 21 | empty |
| 3 | 174 | 0.43 | 0.74 | 30 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2284 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1174 Ų buried · 103 hydrogen bonds · nucleic-nucleic
- A–C · 280 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–D · 277 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–C · 276 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 3JRD · Crystal structure of Fis bound to 27 bp DNA F25 containing T2A3 sequence at center · the same entry in another collection · chain A against A, TM-score 1.00
- P0A6R3 · AlphaFold monomer V2.0 prediction for DNA-binding protein fis (P0A6R3) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 P0A6R3
- Elsewhere: RCSB PDB 3JRD · PDBe 3JRD · UniProt P0A6R3
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