MolNFT v1 · #180058 · protein
Crystal structure of SND1 in complex with C-26-A6
7KNX · Staphylococcal nuclease domain-containing protein 1: “Crystal structure of SND1 in complex with C-26-A6”. X-ray diffraction, 2 ligands (QOV, TYR), 11 pockets (best druggability 0.86). MolNFT v1 #180058 on GenesisL1: 3D structure…
- PDB
- 7KNX
- Type
- protein
- Length
- 1,168 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
- QOV, TYR
- Pockets
- 11 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Staphylococcal nuclease domain-containing protein 1 (EC 3.1.31.1) | protein | 293 | 30% helix, 30% strand | Q7KZF4 |
| B | Staphylococcal nuclease domain-containing protein 1 (EC 3.1.31.1) | protein | 295 | 30% helix, 30% strand | Q7KZF4 |
| C | Staphylococcal nuclease domain-containing protein 1 (EC 3.1.31.1) | protein | 290 | 30% helix, 31% strand | Q7KZF4 |
| D | Staphylococcal nuclease domain-containing protein 1 (EC 3.1.31.1) | protein | 290 | 30% helix, 31% strand | Q7KZF4 |
Ligands and binding sites
- QOV · 5-chloro-2-methoxy-N-(2-methyl[1,2,4]triazolo[1,5-a]pyridin-8-yl)benzene-1-sulfonamide · ligand · 4 copies · chains A, B, D, C
- TYR · Tyrosine · ligand · chains A
- GOL · Glycerol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1086 | 0.86 | 0.87 | 110 | empty |
| 2 | 895 | 0.76 | 0.79 | 66 | QOV |
| 3 | 571 | 0.73 | 0.81 | 58 | QOV |
| 4 | 136 | 0.52 | 0.80 | 18 | empty |
| 5 | 187 | 0.50 | 0.77 | 24 | empty |
Interfaces
4 interfaces between chains.
- B–C · 1111 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 869 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 817 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 144 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7KNX · Crystal structure of SND1 in complex with C-26-A6 · the same entry in another collection · chain D against D, TM-score 1.00
- Q7KZF4 · AlphaFold monomer V2.0 prediction for staphylococcal nuclease domain- containing protein… · a predicted model of the same protein · chain C 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 7KNX · PDBe 7KNX · UniProt Q7KZF4
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