MolNFT v1 · #118920 · protein
Co-crystal structure of NICR2_HSP
5FGL: “Co-crystal structure of NICR2_HSP”. X-ray diffraction, 1 ligand (6HY), 20 pockets (best druggability 0.84). MolNFT v1 #118920 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5FGL
- Type
- protein
- Length
- 1,221 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nicr
- UniProt
- A0A0B4KIF6
- Ligands
- 6HY
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nicr | protein | 200 | 79% helix, 0% strand | A0A0B4KIF6 |
| B, E | Nicr | protein | 206 | 76% helix, 0% strand | A0A0B4KIF6 |
| C | Nicr | protein | 205 | 78% helix, 0% strand | A0A0B4KIF6 |
| D | Nicr | protein | 203 | 78% helix, 0% strand | A0A0B4KIF6 |
| F | Nicr | protein | 201 | 78% helix, 0% strand | A0A0B4KIF6 |
Ligands and binding sites
- 6HY · 4-oxidanylidene-4-(6-oxidanylidene-1~{H}-pyridin-3-yl)butanoic acid · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1015 | 0.84 | 0.85 | 113 | empty |
| 2 | 61 | 0.73 | 0.98 | 18 | 6HY |
| 3 | 743 | 0.72 | 0.78 | 53 | empty |
| 4 | 63 | 0.71 | 0.97 | 18 | 6HY |
| 5 | 61 | 0.71 | 0.97 | 17 | 6HY |
Interfaces
10 interfaces between chains.
- C–D · 2339 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 2311 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 2300 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 485 Ų buried · 7 hydrogen bonds · protein-protein
- D–F · 257 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5FGL · Co-crystal Structure of NicR2_Hsp · 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 A0A0B4KIF6
- Elsewhere: RCSB PDB 5FGL · PDBe 5FGL · UniProt A0A0B4KIF6
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