MolNFT v1 · #180057 · protein
Crystal structure of SND1 in complex with C-26-A2
7KNW · Staphylococcal nuclease domain-containing protein 1: “Crystal structure of SND1 in complex with C-26-A2”. X-ray diffraction, 1 ligand (QOY), 12 pockets (best druggability 0.83). MolNFT v1 #180057 on GenesisL1: 3D structure, binding…
- PDB
- 7KNW
- Type
- protein
- Length
- 1,185 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Staphylococcal nuclease domain-containing protein 1
- EC
- 3.1.31.1
- UniProt
- Q7KZF4
- Ligands
- QOY
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Staphylococcal nuclease domain-containing protein 1 (EC 3.1.31.1) | protein | 298 | 29% helix, 31% strand | Q7KZF4 |
| B | Staphylococcal nuclease domain-containing protein 1 (EC 3.1.31.1) | protein | 295 | 29% helix, 31% strand | Q7KZF4 |
| C, D | Staphylococcal nuclease domain-containing protein 1 (EC 3.1.31.1) | protein | 296 | 29% helix, 31% strand | Q7KZF4 |
Ligands and binding sites
- QOY · 5-chloro-2-methoxy-N-([1,2,4]triazolo[1,5-a]pyridin-8-yl)benzene-1-sulfonamide · ligand · 4 copies · chains A, D, B, C
- GOL · Glycerol · additive · 3 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1006 | 0.83 | 0.84 | 97 | GOL |
| 2 | 778 | 0.76 | 0.81 | 61 | QOY |
| 3 | 698 | 0.75 | 0.81 | 69 | QOY |
| 4 | 260 | 0.71 | 0.86 | 52 | empty |
| 5 | 184 | 0.55 | 0.80 | 22 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1098 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1015 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 909 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 125 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7KNW · Crystal structure of SND1 in complex with C-26-A2 · the same entry in another collection · chain A against A, TM-score 1.00
- Q7KZF4 · AlphaFold monomer V2.0 prediction for staphylococcal nuclease domain- containing protein… · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q7KZF4
- Elsewhere: RCSB PDB 7KNW · PDBe 7KNW · UniProt Q7KZF4
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