MolNFT v1 · #158026 · protein
Single particle reconstruction of darpin and its bound GFP on a symmetric scaffold
6NHV · Superfolder GFP: “Single particle reconstruction of darpin and its bound GFP on a symmetric scaffold”. Electron microscopy, 1 ligand (CRO), 16 pockets (best druggability 0.81). MolNFT v1 #158026 on GenesisL1: 3D structure, binding…
- PDB
- 6NHV
- Type
- protein
- Length
- 1,165 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Superfolder GFP; DARP14 - subunit B; Subunit a-darpin
- UniProt
- Q9I2D8
- Ligands
- CRO
- Pockets
- 16 · best druggability 0.81
Structure
electron microscopy · 4 distinct chains · 46% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Superfolder GFP | protein | 228 | 11% helix, 52% strand | — |
| N, O, X | DARP14 - subunit B | protein | 118 | 24% helix, 36% strand | Q9I2D8 |
| R | Subunit a-darpin | protein | 297 | 66% helix, 0% strand | — |
| S, T | Subunit a-darpin | protein | 143 | 78% helix, 0% strand | — |
Ligands and binding sites
- CRO · {2-[(1R,2R)-1-amino-2-hydroxypropyl]-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 662 | 0.81 | 0.86 | 48 | empty |
| 2 | 81 | 0.75 | 0.98 | 23 | CRO |
| 3 | 434 | 0.68 | 0.80 | 60 | empty |
| 4 | 307 | 0.63 | 0.80 | 47 | empty |
| 5 | 162 | 0.57 | 0.81 | 30 | empty |
Interfaces
11 interfaces between chains.
- N–X · 1289 Ų buried · 25 hydrogen bonds · protein-protein
- N–O · 1271 Ų buried · 23 hydrogen bonds · protein-protein
- O–X · 1257 Ų buried · 21 hydrogen bonds · protein-protein
- A–R · 904 Ų buried · 7 hydrogen bonds · protein-protein
- R–S · 792 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (chromophore).
Compared structures
- 6NHV · Single particle reconstruction of DARPin and its bound GFP on a symmetric scaffold · 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 Q9I2D8
- Elsewhere: RCSB PDB 6NHV · PDBe 6NHV · UniProt Q9I2D8
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