MolNFT v1 · #103323 · protein
Structure of vccnt-7C8C bound to adenosine
4PD9 · Nupc family protein: “Structure of vccnt-7C8C bound to adenosine”. X-ray diffraction, 2 ligands (ADN, NA), 5 pockets (best druggability 0.66). MolNFT v1 #103323 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4PD9
- Type
- protein
- Length
- 404 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nupc family protein
- UniProt
- Q9KPL5
- Ligands
- ADN, NA
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nupc family protein | protein | 404 | 77% helix, 0% strand | Q9KPL5 |
Ligands and binding sites
- ADN · Adenosine · ligand · chains A
- NA · Sodium ion · metal · chains A
- DMU · Decyl-beta-D-maltopyranoside · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 412 | 0.66 | 0.79 | 41 | ADN |
| 2 | 144 | 0.61 | 0.84 | 20 | empty |
| 3 | 147 | 0.46 | 0.76 | 22 | empty |
| 4 | 66 | 0.30 | 0.73 | 13 | empty |
| 5 | 52 | 0.29 | 0.75 | 13 | empty |
Compared structures
- 4PD9 · Structure of vcCNT-7C8C bound to adenosine · 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 Q9KPL5
- Elsewhere: RCSB PDB 4PD9 · PDBe 4PD9 · UniProt Q9KPL5
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