MolNFT v1 · #28416 · protein
X-ray structure of northeast structural genomics target SR44
1YDM · Hypothetical protein yqgn: “X-ray structure of northeast structural genomics target SR44”. X-ray diffraction, 1 ligand (SO4), 7 pockets (best druggability 0.85). MolNFT v1 #28416 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 1YDM
- Type
- protein
- Length
- 542 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein yqgn
- UniProt
- P54491
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hypothetical protein yqgn | protein | 178 | 30% helix, 18% strand | P54491 |
| B | Hypothetical protein yqgn | protein | 182 | 32% helix, 17% strand | P54491 |
| C | Hypothetical protein yqgn | protein | 182 | 32% helix, 18% strand | P54491 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 822 | 0.85 | 0.88 | 76 | SO4 |
| 2 | 359 | 0.64 | 0.79 | 42 | empty |
| 3 | 264 | 0.55 | 0.77 | 38 | SO4 |
| 4 | 98 | 0.54 | 0.84 | 24 | empty |
| 5 | 226 | 0.48 | 0.74 | 25 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1298 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 311 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 91 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
- 1YDM · X-Ray structure of Northeast Structural Genomics target SR44 · the same entry in another collection · chain A against A, TM-score 1.00
- P54491 · AlphaFold monomer V2.0 prediction for uncharacterized protein yqgn (P54491) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 P54491
- Elsewhere: RCSB PDB 1YDM · PDBe 1YDM · UniProt P54491
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