MolNFT v1 · #56287 · protein
Crystal structure of the soluble domain of STT3 from P. furiosus
2ZAI · Oligosaccharyl transferase STT3 subunit related protein: “Crystal structure of the soluble domain of STT3 from P. furiosus”. X-ray diffraction, 2 ligands (CA, CL), 20 pockets (best druggability 0.75). MolNFT v1 #56287 on GenesisL1…
- PDB
- 2ZAI
- Type
- protein
- Length
- 1,881 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oligosaccharyl transferase STT3 subunit related protein
- UniProt
- Q8U4D2
- Ligands
- CA, CL
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 19% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oligosaccharyl transferase STT3 subunit related protein | protein | 472 | 20% helix, 47% strand | Q8U4D2 |
| B | Oligosaccharyl transferase STT3 subunit related protein | protein | 468 | 18% helix, 46% strand | Q8U4D2 |
| C | Oligosaccharyl transferase STT3 subunit related protein | protein | 470 | 18% helix, 43% strand | Q8U4D2 |
| D | Oligosaccharyl transferase STT3 subunit related protein | protein | 471 | 21% helix, 47% strand | Q8U4D2 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 934 | 0.75 | 0.78 | 72 | CL |
| 2 | 881 | 0.73 | 0.77 | 88 | empty |
| 3 | 892 | 0.73 | 0.77 | 102 | empty |
| 4 | 340 | 0.68 | 0.82 | 31 | empty |
| 5 | 424 | 0.67 | 0.79 | 37 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1398 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1367 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 1006 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2ZAI · Crystal structure of the soluble domain of STT3 from P. furiosus · the same entry in another collection · chain D against D, TM-score 1.00
- Q8U4D2 · AlphaFold monomer V2.0 prediction for dolichyl- phosphooligosaccharide-protein… · a predicted model of the same protein · chain D against A, TM-score 0.98
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 Q8U4D2
- Elsewhere: RCSB PDB 2ZAI · PDBe 2ZAI · UniProt Q8U4D2
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