MolNFT v1 · #136417 · protein
Crystal structure of mccf-like protein (BA_5613) in the complex with aspartyl sulfamoyl adenylate
5USD · Peptidase S66: “Crystal structure of mccf-like protein (BA_5613) in the complex with aspartyl sulfamoyl adenylate”. X-ray diffraction, 1 ligand (DSZ), 12 pockets (best druggability 0.80). MolNFT v1 #136417 on GenesisL1: 3D…
- PDB
- 5USD
- Type
- protein
- Length
- 1,318 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidase S66
- UniProt
- Q81JT5
- Ligands
- DSZ
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Peptidase S66 | protein | 329 | 34% helix, 24% strand | Q81JT5 |
| B, D | Peptidase S66 | protein | 330 | 34% helix, 23% strand | Q81JT5 |
Ligands and binding sites
- DSZ · 5'-O-(L-alpha-aspartylsulfamoyl)adenosine · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains A, C
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 | 988 | 0.80 | 0.81 | 110 | DSZ |
| 2 | 878 | 0.79 | 0.82 | 91 | DSZ |
| 3 | 92 | 0.58 | 0.87 | 22 | empty |
| 4 | 83 | 0.56 | 0.86 | 21 | empty |
| 5 | 82 | 0.55 | 0.86 | 22 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1833 Ų buried · 32 hydrogen bonds · protein-protein
- A–D · 1830 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 517 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified (engineered).
Compared structures
- 5USD · Crystal structure of MccF-like protein (BA_5613) in the complex with aspartyl sulfamoyl… · 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 Q81JT5
- Elsewhere: RCSB PDB 5USD · PDBe 5USD · UniProt Q81JT5
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