MolNFT v1 · #122116 · protein
Human nono (P54NRB) homodimer
5IFM · Non-pou domain-containing octamer-binding protein: “Human nono (P54NRB) homodimer”. X-ray diffraction, 3 ligands (PRO, K, CL), 20 pockets (best druggability 0.86). MolNFT v1 #122116 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5IFM
- Type
- protein
- Length
- 3,077 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-pou domain-containing octamer-binding protein
- UniProt
- Q15233
- Ligands
- PRO, K, CL
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 7 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Non-pou domain-containing octamer-binding protein | protein | 254 | 37% helix, 25% strand | Q15233 |
| B, J, K | Non-pou domain-containing octamer-binding protein | protein | 259 | 39% helix, 24% strand | Q15233 |
| C, E | Non-pou domain-containing octamer-binding protein | protein | 256 | 40% helix, 24% strand | Q15233 |
| D | Non-pou domain-containing octamer-binding protein | protein | 257 | 38% helix, 24% strand | Q15233 |
| F | Non-pou domain-containing octamer-binding protein | protein | 255 | 39% helix, 24% strand | Q15233 |
| G, I, L | Non-pou domain-containing octamer-binding protein | protein | 255 | 40% helix, 24% strand | Q15233 |
| H | Non-pou domain-containing octamer-binding protein | protein | 257 | 39% helix, 24% strand | Q15233 |
Ligands and binding sites
- PRO · Proline · ligand · 2 copies · chains A, B, C
- K · Potassium ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 10 copies · chains A, E, C, G, D, F, I, H, K, L
- GOL · Glycerol · additive · 5 copies · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 958 | 0.86 | 0.87 | 110 | CL |
| 2 | 408 | 0.81 | 0.89 | 59 | CL |
| 3 | 315 | 0.78 | 0.89 | 53 | CL |
| 4 | 392 | 0.78 | 0.87 | 40 | GOL |
| 5 | 278 | 0.77 | 0.89 | 45 | CL |
Interfaces
26 interfaces between chains.
- E–F · 5400 Ų buried · 90 hydrogen bonds · protein-protein
- I–J · 5376 Ų buried · 92 hydrogen bonds · protein-protein
- K–L · 5324 Ų buried · 89 hydrogen bonds · protein-protein
- C–D · 5312 Ų buried · 91 hydrogen bonds · protein-protein
- G–H · 5282 Ų buried · 86 hydrogen bonds · protein-protein
Compared structures
- 5IFM · Human NONO (p54nrb) Homodimer · the same entry in another collection · chain L against L, 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 Q15233
- Elsewhere: RCSB PDB 5IFM · PDBe 5IFM · UniProt Q15233
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