MolNFT v1 · #56285 · protein
Crystal structure of the semet-substituted soluble domain of STT3 from P. furiosus
2ZAG · Oligosaccharyl transferase STT3 subunit related protein: “Crystal structure of the semet-substituted soluble domain of STT3 from P. furiosus”. X-ray diffraction, 2 ligands (CA, CL), 20 pockets (best druggability 0.79). MolNFT v1…
- PDB
- 2ZAG
- Type
- protein
- Length
- 1,913 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 0.79
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Oligosaccharyl transferase STT3 subunit related protein | protein | 478 | 20% helix, 44% strand | Q8U4D2 |
| B | Oligosaccharyl transferase STT3 subunit related protein | protein | 477 | 19% helix, 47% strand | Q8U4D2 |
| D | Oligosaccharyl transferase STT3 subunit related protein | protein | 480 | 19% helix, 43% 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1117 | 0.79 | 0.80 | 104 | CL |
| 2 | 268 | 0.76 | 0.89 | 31 | empty |
| 3 | 303 | 0.75 | 0.88 | 34 | empty |
| 4 | 277 | 0.74 | 0.87 | 31 | empty |
| 5 | 846 | 0.71 | 0.76 | 77 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1408 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1377 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 999 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified, 4 disulfide (engineered, disulfide).
Compared structures
- 2ZAG · Crystal structure of the SeMet-substituted 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 2ZAG · PDBe 2ZAG · UniProt Q8U4D2
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