MolNFT v1 · #140397 · protein
Crystal structure of safdaa-dsc complex
5Y9H · SAFD,PUTATIVE outer membrane PROTEIN,PUTATIVE outer…: “Crystal structure of safdaa-dsc complex”. X-ray diffraction, 11 pockets (best druggability 0.84). MolNFT v1 #140397 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5Y9H
- Type
- protein
- Length
- 1,275 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SAFD,PUTATIVE outer membrane PROTEIN,PUTATIVE outer membrane PROTEIN,PUTATIVE outer…
- UniProt
- H9L4M7, Q8ZRK4
- Pockets
- 11 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 2% helix, 56% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SAFD,PUTATIVE outer membrane PROTEIN,PUTATIVE outer membrane PROTEIN,PUTATIVE outer membrane protein | protein | 430 | 1% helix, 56% strand | H9L4M7, Q8ZRK4 |
| B | SAFD,PUTATIVE outer membrane PROTEIN,PUTATIVE outer membrane PROTEIN,PUTATIVE outer membrane protein | protein | 424 | 2% helix, 55% strand | H9L4M7, Q8ZRK4 |
| C | SAFD,PUTATIVE outer membrane PROTEIN,PUTATIVE outer membrane PROTEIN,PUTATIVE outer membrane protein | protein | 421 | 2% helix, 56% strand | H9L4M7, Q8ZRK4 |
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1037 | 0.84 | 0.85 | 97 | empty |
| 2 | 960 | 0.69 | 0.74 | 89 | empty |
| 3 | 282 | 0.51 | 0.74 | 38 | empty |
| 4 | 65 | 0.49 | 0.85 | 17 | empty |
| 5 | 108 | 0.49 | 0.80 | 23 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1693 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 610 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 67 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5Y9H · Crystal structure of SafDAA-dsc complex · 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 H9L4M7
- Every structure of UniProt Q8ZRK4
- Elsewhere: RCSB PDB 5Y9H · PDBe 5Y9H · UniProt H9L4M7 · UniProt Q8ZRK4
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