Research workbench
Structure of pentameric S-layer protein from halofaerax volcanii
Analyse Structure of pentameric S-layer protein from halofaerax volcanii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PTU
- Type
- protein
- Length
- 2,370 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell surface glycoprotein
- UniProt
- P25062
- Ligands
- BGC
- Pockets
- 20 · best druggability 0.71
Structure
electron microscopy · 1 distinct chain · 8% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Cell surface glycoprotein | protein | 474 | 8% helix, 37% strand | P25062 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 5 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 661 | 0.71 | 0.79 | 46 | empty |
| 2 | 1004 | 0.71 | 0.75 | 111 | empty |
| 3 | 57 | 0.70 | 0.97 | 23 | empty |
| 4 | 925 | 0.70 | 0.75 | 104 | empty |
| 5 | 55 | 0.70 | 0.97 | 19 | empty |
Interfaces
5 interfaces between chains.
- D–E · 926 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 925 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 924 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 923 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 913 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 glycan (N-glycosylation).
Compared structures
- 7PTU · Structure of pentameric S-layer protein from Halofaerax volcanii · the same entry in another collection · chain E against E, TM-score 1.00
- P25062 · AlphaFold monomer V2.0 prediction for cell surface glycoprotein (P25062) · a predicted model of the same protein · chain B against A, TM-score 0.76
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 P25062
- Elsewhere: RCSB PDB 7PTU · PDBe 7PTU · UniProt P25062
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