MolNFT v1 · #104827 · protein
The structure of mtdh-SND1 complex reveals novel cancer-promoting interactions
4QMG · Staphylococcal nuclease domain-containing protein 1: “The structure of mtdh-SND1 complex reveals novel cancer-promoting interactions”. X-ray diffraction, 2 ligands (CS, SO4), 15 pockets (best druggability 0.81). MolNFT v1 #104827 on…
- PDB
- 4QMG
- Type
- protein
- Length
- 1,619 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Staphylococcal nuclease domain-containing protein 1; Protein lyric
- UniProt
- Q7KZF4, Q86UE4
- Ligands
- CS, SO4
- Pockets
- 15 · best druggability 0.81
Structure
x-ray diffraction · 9 distinct chains · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Staphylococcal nuclease domain-containing protein 1 | protein | 311 | 29% helix, 29% strand | Q7KZF4 |
| F, J | Protein lyric | protein | 13 | 0% helix, 0% strand | Q86UE4 |
| B | Staphylococcal nuclease domain-containing protein 1 | protein | 309 | 27% helix, 30% strand | Q7KZF4 |
| G | Protein lyric | protein | 15 | 0% helix, 0% strand | Q86UE4 |
| C | Staphylococcal nuclease domain-containing protein 1 | protein | 306 | 29% helix, 30% strand | Q7KZF4 |
| H | Protein lyric | protein | 17 | 0% helix, 0% strand | Q86UE4 |
| D | Staphylococcal nuclease domain-containing protein 1 | protein | 311 | 26% helix, 29% strand | Q7KZF4 |
| I | Protein lyric | protein | 15 | 0% helix, 0% strand | Q86UE4 |
| E | Staphylococcal nuclease domain-containing protein 1 | protein | 309 | 28% helix, 31% strand | Q7KZF4 |
Ligands and binding sites
- CS · Cesium ion · metal · 5 copies · chains A, B, C, D, E
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C, D, E
- GOL · Glycerol · additive · 4 copies · chains B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 929 | 0.81 | 0.82 | 76 | empty |
| 2 | 1050 | 0.80 | 0.81 | 84 | SO4 |
| 3 | 306 | 0.60 | 0.78 | 30 | SO4, GOL |
| 4 | 272 | 0.59 | 0.78 | 25 | SO4, GOL |
| 5 | 170 | 0.57 | 0.81 | 29 | empty |
Interfaces
13 interfaces between chains.
- A–B · 1417 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1304 Ų buried · 13 hydrogen bonds · protein-protein
- C–H · 1030 Ų buried · 14 hydrogen bonds · protein-protein
- E–J · 1023 Ų buried · 16 hydrogen bonds · protein-protein
- D–I · 983 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 23 modified (engineered).
Compared structures
- 4QMG · The Structure of MTDH-SND1 Complex Reveals Novel Cancer-Promoting Interactions · the same entry in another collection · chain J against J, TM-score 1.00
- Q7KZF4 · AlphaFold monomer V2.0 prediction for staphylococcal nuclease domain- containing protein… · a predicted model of the same protein · chain D 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 Q7KZF4
- Every structure of UniProt Q86UE4
- Elsewhere: RCSB PDB 4QMG · PDBe 4QMG · UniProt Q7KZF4 · UniProt Q86UE4
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