MolNFT v1 · #123958 · protein
Crystal structure of the archaeosine synthase quef-like in the apo form
5K0P · Archeaosine synthase quef-like: “Crystal structure of the archaeosine synthase quef-like in the apo form”. X-ray diffraction, 1 ligand (SCN), 20 pockets (best druggability 0.76). MolNFT v1 #123958 on GenesisL1: 3D structure, binding…
- PDB
- 5K0P
- Type
- protein
- Length
- 1,008 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Archeaosine synthase quef-like
- UniProt
- A3MSP1
- Ligands
- SCN
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 25% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Archeaosine synthase quef-like | protein | 103 | 24% helix, 42% strand | A3MSP1 |
| B, E, J | Archeaosine synthase quef-like | protein | 100 | 25% helix, 42% strand | A3MSP1 |
| C, D, F, G | Archeaosine synthase quef-like | protein | 101 | 25% helix, 42% strand | A3MSP1 |
| H | Archeaosine synthase quef-like | protein | 99 | 25% helix, 40% strand | A3MSP1 |
| I | Archeaosine synthase quef-like | protein | 102 | 25% helix, 41% strand | A3MSP1 |
Ligands and binding sites
- SCN · Thiocyanate ion · ion · 10 copies · chains A, B, C, G, D, E, F, H, I, J
- PGE · Triethylene glycol · additive · 3 copies · chains C, H, B, D, F, G
- PG4 · Tetraethylene glycol · additive · chains A, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 409 | 0.76 | 0.86 | 61 | empty |
| 2 | 477 | 0.76 | 0.84 | 57 | PGE |
| 3 | 154 | 0.75 | 0.93 | 30 | empty |
| 4 | 114 | 0.70 | 0.92 | 19 | empty |
| 5 | 150 | 0.70 | 0.90 | 29 | empty |
Interfaces
20 interfaces between chains.
- C–G · 747 Ų buried · 13 hydrogen bonds · protein-protein
- I–J · 729 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 729 Ų buried · 12 hydrogen bonds · protein-protein
- B–I · 718 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 708 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5K0P · Crystal structure of the archaeosine synthase QueF-Like in the apo form · the same entry in another collection · chain J against J, TM-score 1.00
- A3MSP1 · AlphaFold monomer V2.0 prediction for archaeosine synthase (A3MSP1) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 A3MSP1
- Elsewhere: RCSB PDB 5K0P · PDBe 5K0P · UniProt A3MSP1
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